Patent Publication Number: US-2007105105-A1

Title: Surrogate cell gene expression signatures for evaluating the physical state of a subject

Description:
This application claims priority from U.S. Provisional Patent Application No. 60/473,089, filed May 23, 2003, which is herein incorporated by reference in its entirety. 
    
    
      The research leading to this invention was supported, in part, by Grant No. 1RO3 MH62428-01 awarded by the National Institutes of Mental Health. Accordingly, the United States government may have certain rights to this invention. 
    
    
     FIELD OF THE INVENTION  
      The present invention relates to non-invasive and minimally invasive techniques for evaluating the physical state of a subject, including diagnosing a disease, disorder, or physical state of the subject, determining the prognosis of the subject, determining a subject&#39;s susceptibility for a disease, disorder, or physical state and determining, developing and monitoring treatment for the same. The invention also relates to identifying genetic alterations contributing to, or susceptibility for, development of a disease, disorder, or physical state, and for diagnosis, prognosis and treatment of the disease, disorder, or physical state.  
     BACKGROUND OF THE INVENTION  
      Although cancer mortality rates have decreased over the past decade, through pre-symptomatic screening programs and major improvements in cancer treatment, survival rates are still low in patients presenting with a more advanced stage cancer at the time of diagnosis. Thus, effective management of any cancer relies heavily on an early diagnosis, coupled with a need to obtain accurate information on the classification and stage of the cancer itself, and thus limitations of traditional diagnostic and prognostic techniques may currently hinder the management of cancer.  
      Current techniques for the screening and risk assessment of chronic disease states in general, and cancer in particular, are frequently based upon the measurement of either individual serum biomarkers, or expression of individual genes in circulating cells, such as disseminated tumor cells. In disease states for which such non-invasive tests are available they usually comprise a prerequisite to more invasive, surgical biopsy procedures.  
      Examples of serum biomarkers used in the clinical diagnosis of cancer include CA 125 (ovarian cancer), CA 15-3 and CA 27-29 (breast cancer), carcinoembryonic antigen, CEA (ovarian, lung, breast, pancreas, and gastrointestinal tract cancers), prostate specific antigen, PSA (prostate cancer), alpha fetoprotein, AFP (primary liver cancer or germ cell cancer), human chorionic gonadotropin, HCG (choriocarcinoma, cancers of the testis, ovary, liver, stomach, pancreas, and lung) CA 19-9 (colorectal cancer pancreatic, stomach, and bile duct cancer) neuron-specific enolase, NSE (neuroblastoma; small cell lung cancer; Wilms&#39; tumor; melanoma; and cancers of the thyroid, kidney, testicle, and pancreas (Source: National Cancer Institute, on the Worldwide Web at nci.nih.gov)  
      Diagnosis of psychiatric and neurological diseases for which the molecular etiology is largely unknown, such as schizophrenia or not too well understood such as in Alzheimer&#39;s disease, still depend mainly on behavioral evaluation of patients, and no clinically proven, blood-based, tests are available to date. Individual circulating biomarkers, however, are beginning to be discovered. In Alzheimer&#39;s disease, for instance, a serum elevation of the iron transporter p97 (Kim D K, et al. Neuropsychopharmacology 2001; 25(1):84-90) or an increase in antibody-mediated brain to plasma amyloid-beta efflux (DeMattos R B, et al., Science 2002, 295:2264-2267) have been described. Furthermore, Ilani et al. have shown an increased level of D3 dopamine receptor mRNA in circulating blood lymphocytes in individuals with schizophrenia (Ilani et al. Proc Natl Acad Sci USA 2001; 98(2):625-8).  
      For cancer, diagnostic tests based on single circulating biomarkers possess a number of limitations, including lack of specificity and sensitivity in the diagnosis and, also a lack of prognostic information. This ultimately yields high numbers of false positive diagnoses, and consequently unnecessarily large numbers of surgical biopsies. Alternatively, in a significant number of patients malignancies evade detection due to the inherent rate of false negative test results.  
      There is growing evidence that individuals with a malignant disease such as breast cancer or prostate cancer, exhibit immune responses that can be detected at the level of altered gene expression in leukocytes circulating in peripheral blood. Quantitation of the mRNA transcripts in leukocytes of a number of individual genes has demonstrated associations between gene expression levels and the presence of a tumor in patients with breast and prostate cancer.  
      The recent development of microarray technology has permitted simultaneous measurement of the expression levels of thousands of genes, and also allowed a comparison of multiple data sets between multiple experiments. Investigators have begun to employ this technology, based upon sample cDNA probe hybridization to DNA-based microarrays, to identify and isolate genes differentially expressed among many tissues and cell lines. Microarray technology will become a global gene expression diagnostic tool (Cole et al., Nat. Genet. 1999: 21(1 Suppl):38-1; Howell S B, Mol Urol. 1999; 3(3):295-300). Already, breakthrough experiments have shown that molecular profiles, or gene expression signatures, can be deduced from microarray expression analysis of tumor samples. Researchers have used statistical algorithms to compare individual expression signatures, and then employed these comparisons to distinguish between forms of myeloid leukemia (Golub et al., Science 1999; 286(5439):531-7), and B-cell lymphoma (Alizadeh et al, Nature 2000; 403(6769):503-11). Furthermore, analysis of tumor tissue from individual patients has permitted identification of both stages and individual classes of breast cancer (Perou et al., Nature 2000; 406(6797):747-52), malignant melanoma (Bittner et al., Nature 2000; 406(6795):536-40), and prostate cancer (Dhanasekaran et al., Nature 2001; 412(6849):822-6; Luo et al., Mol Carcinog 2002; 33(1):25-35). Additionally, utilizing microarray technology van&#39;t Veer et al., have shown that the clinical status and clinical outcome of breast cancer can be predicted by gene expression analysis of tumor tissue (Nature 2002; 415(6871):530-6).  
      Even at this early stage in the clinical development of this technology, it is becoming clear that microarray analysis will be able to provide important diagnostic and prognostic information for many tumor types. However, although these investigations of solid tumors provide detailed information on the pathology and malignant process of the tumor, invasive surgery or biopsy is always necessary to obtain the tumor tissue studied, and although investigations are underway to determine the feasibility of minimally traumatic biopsy sampling procedures for obtaining tissue for microarray analysis, a current report documents problems such as very low yields of extracted RNA (Assersohn et al., Clin Cancer Res. 2002; 8(3):794-801).  
      A link between cancer and altered gene expression in the immune system has been previously documented. Tumor-induced immunosuppression allows malignant cells to evade the immune system, and some tumors are commonly found in individuals with compromised immune function. For example, Karposi&#39;s sarcoma has become a very common and highly aggressive neoplastic complication of AIDS (Ensoli &amp; Sirianni., Crit Rev Oncog 1998; 9(2):107-24), and it has been proposed that chronic inflammation, resulting from infective and/or non-infective agents, may provide the ideal environment for the cellular development of cancer (O&#39;Byrne &amp; Dagleish, Br J Cancer 2001; 85(4):473-83).  
      Many mechanisms are thought to be involved in the altered immune response of cancer patients. These include decreased natural killer (NK) cell cytotoxicity (Kono et al., Clin Cancer Res. 1996; 2(11): 1825-8), the production in the tumor of cytokines and growth factors that have known suppressive effects on leukocyte function (e.g. interleukin 6 (IL-6), IL4 and TGF-beta1), (Oliver and Nouri., Cancer Surv. 1992; 173-204), and defective cytokine release from T-cells, such as a decrease in IL-2 (Lopez et al., Cell Immunol. 1998; 190(2):141-55).  
      Research to further elucidate the immune responses observed in cancer patients has mainly focused on measuring the level of genes or protein products from cells within the microenvironment of the tumor, such as IL-2 mRNA transcript levels in tumor infiltrating lymphocytes within primary human breast carcinomas (Lopez et al., 1998) and adenocarcinomas of the prostate (Elsasser-Beile et al., J. Cancer Res Clin Oncol. 1993; 119(7):430-3). However, a number of groups have also reported altered levels of the mRNA and/or protein products of individual genes in leukocyte cells within the circulating peripheral blood of cancer patients.  
      Veltri and colleagues have reported that IL-8 mRNA expression is up-regulated in patients with metastatic prostate cancer relative to control subjects (Veltri et al., Urology 1999; 53(1):139-47). Specifically, these investigators carried out an analysis of IL-8 mRNA levels in peripheral blood from metastatic patients and normal control subjects (pooled into one sample), employing IL-8 gene specific primers for RT-PCR experiments, and 25 cycles of amplification in the PCR. The results documented the presence of IL-8 products in all metastatic prostate cancer patient samples, while in the pool of control samples no amplification of IL-8 was observed (Veltri et al., 1999). As discussed below, the present inventors have performed similar experiments to seek to confirm these results.  
      Recently, a study was initiated to investigate expression levels of the mismatch repair genes, MSH2 and MLH1 in prostate cancer (Strom et al., Prostate 2001; 1; 47(4):269-75). Strom et al., performed RT-PCR analysis of leukocyte samples from 70 prostate cancer subjects (metastatic patients were excluded from this study), and 97 matched controls. Their results implied that although considerable variation occurred among patients, the mean expression levels for both genes were significantly lower in the patients than controls. Although the authors conclude that decreased expression of MLH1 is a risk factor for prostate cancer, they also state that the decreased expression of both genes may be caused by disease status, a conclusion that is consistent with this hypothesis. The present invention provides preliminary data that reproduces these results. Veltri et al., further reported that increasing concentrations of serum IL-8 protein could be positively correlated with increasing tumor burden, and that serum IL-8 levels correctly distinguished among patients classified to one of four known stages of prostate cancer (Veltri et al., 1999). Additionally, the authors reported unpublished data showing that quantitative RT-PCR analysis of IL-6 and IL-10 mRNA levels also yielded a marked difference between prostate cancer patients and control subjects, and these results have been published by Ralph et al., (U.S. Pat. No. 6,190,857). Earlier studies that have measured serum levels of IL-6 and IL-10 proteins in cancer patients support these observations. Specifically, IL-6 serum levels have been shown to provide prognostic information on prostate tumors (Nakashima et al., Cancer Res. 2000; 6(7):2702-6), and serum IL-10 levels have been correlated with the presence of a prostate tumor (Filella et al., Prostate 2000; 44(4):2714). A decrease in IL-10 serum levels has also been reported to be a prognostic indicator for multiple advanced solid tumors (De Vita et al., Oncol Rep. 2000; 7(2):357-61). In addition to these cytokine investigations, studies by Elsasser-Beile et al., 1993, supra have indicated that decreasing levels of serum IFN gamma protein correlate with increasing prostate tumor mass (Elsasser-Beile et al., 1993), and the present inventors have detected mRNA levels of IFN-gamma in peripheral blood leukocytes that are consistent with this study ( ). The diseases described above, such as schizophrenia and cancer, can be considered complex disorders, in as much as multiple gene abnormalities contribute to the etiology. Genome scans are widely used in the search for linkage regions, as a prerequisite for identification and mutation screening of candidate susceptibility genes. Linkage studies possess a number of limitations, often including some lack of reproducible, strong linkage findings, and the large breadth of chromosomal areas identified, which can contain potentially hundreds of genes. It is also considered that multiple genes of small or moderate effect may contribute to for example schizophrenia susceptibility, and therefore each need to be identified. However, linkage studies have highlighted a number of chromosomal regions that may harbor genes that contribute to schizophrenia and cancer. The difficult task is to identify susceptibility alleles among the large numbers of genes within or near these regions. Sequence analysis and association testing for all the genes within regions of linkage would be an overwhelming task.  
      An alternatively investigation of candidate genes that does not rely on genetic linkage data, allows a potential direct route to discovery of a gene mutation that may be involved in the etiology and pathogenesis of a disease, for example schizophrenia (O&#39;Donovan et al., Am J Hum Genet 1999; 65, 587-592). To date however, although plausible candidates, particularly neurotransmitter metabolism and transport pathway members, and genes implicated in neurodevelopment, have been investigated, no candidate gene to date has produced strong association with schizophrenia.  
      A few recent studies have explored the possibility of finding candidate genes for complex disorders and/or traits, by involving a paradigm of candidate gene discovery or identification within regions of linkage, following or in parallel with measurement of gene expression of the tissue of interest. The paradigm of utilizing gene expression for the identification of candidate disease genes was also explored by Blackshaw et al. in a study of gene expression in murine rod cells, to identify gene candidates for retinal diseases (Blackshaw et al., Cell 2001; 107:579-89). The study, performed by serial analysis of gene expression (SAGE) found 264 previously uncharacterized genes that were expressed in the rod cells. Of those, 87 mapped to 37 different retinal disease loci, and are therefore considered candidate disease genes. In another study, Oestreicher et al. performed microarray gene expression using biopsied skin from patients with psoriasis and healthy controls and found 159 genes that were differentially expressed in the psoriasis biopsy samples. 27 of the differentially expressed genes mapped to psoriasis susceptibility loci, and were then considered as candidate genes for psoriasis (Oestreicher et al., Pharmacogenomics J. 2001; 1(4):272-87). Additional problems with this approach however, are that for the analysis of, for example brain tissue for research in psychiatric disorders such as schizophrenia, research problems are encountered by investigators collecting post mortem brain samples, where the subject&#39;s physiological state at death can be poorly defined, and the delay between time of death and brain sample collection can be lengthy (Li et al., Hum Mol Genet. 2004 13(6):609-16). This can lead to variability between samples, as also recently reported by Loring et al., following a study of gene expression in brain tissue from Alzheimer&#39;s disease patients (Loring et al., DNA Cell Biol. 2001; 20:683-95). In addition, biopsy would also be required for the analysis of tumor tissue for cancer research, and thus many subjects would have to undergo additional invasive surgery to obtain tissues for study.  
     SUMMARY OF THE INVENTION  
      In one embodiment, the invention provides a method for evaluating a physical state of a subject (e.g., a “test subject”). This method comprises comparing an expression profile of surrogate cells from the subject, with a normal expression profile of surrogate cells from a normal subject not having the physical state, wherein a difference between the expression profiles is indicative of the physical state of the test subject.  
      In an alternative embodiment, evaluating a physical state of a subject (e.g., a “test subject”), which method involves comparing an expression profile of surrogate cells from the test subject with an expression profile of surrogate cells from a known subject or subjects determined to have the physical state. In this case, similarity in the expression profiles indicates that the test subject has the physical state of the known subject or subjects  
      In yet another embodiment, the invention provides a method for evaluating a treatment or therapy, such as a therapeutic compound, in a test subject. This method comprises comparing an expression profile of surrogate cells from the subject after exposing the subject to the compound, with an expression profile of surrogate cells from the subject prior to exposure to the compound, wherein a difference in the expression profiles indicates an effect of the compound on the test subject. In a further aspect, this method compares the expression profile of the test subject after exposing the subject to the compound, with a normal expression profile of surrogate cells from a normal subject. Similarity of the expression profiles indicates a therapeutic benefit of the compound.  
      In yet another aspect, this method compares the expression profile of the test subject after exposing the subject to the treatment or therapy, with an expression profile of surrogate cells from other subjects with the same physical state following exposure to different therapies and improvement of physical state, wherein a similarity of the expression profiles is indicative of the treatment or therapy efficacy on the test subject. In another alternative method, the expression profile of the test subject after exposing the subject to the treatment or therapy, is compared with an expression profile of surrogate cells from other subjects with the same physical state following exposure to different therapies, and lack of improvement or worsening of the physical state. Similarity of the expression profiles indicates a lack of therapeutic benefit of the compound.  
      In yet another embodiment, the invention provides a method for predicting a response to treatment or therapy, which comprises comparing an expression profile from the test subject prior to exposing the subject to a treatment or therapy, with an expression profile from surrogate cells from other subjects with the same physical state also profiled prior to exposure to different therapies, wherein a similarity in the expression profiles predicts an effect of the treatment or therapy on the test subject based on the effect of that therapy on another subject or subjects having a similar pre-treatment expression profile. In a further aspect, this method would be employed for choice of treatments.  
      In yet another embodiment the present invention provides for a method of treating a disease, disorder or physical state or to prevent onset of a disease, disorder or physical state, comprising administering a nucleic acid found to have altered expression in surrogate tissues, between a test subjects with the physical state, and a normal subject or subjects, including, but not limited to gene therapy with nucleic acid transcripts, antisense mRNA, or other inhibitory RNAs.  
      In an additional embodiment, this invention provides a method for identifying nucleic acids containing sequence alterations that may have a role in the etiology of a disease or disorder or physical state, in the pathogenesis of, or in the susceptibility for developing a disease or disorder or physical state. This method comprises identifying a nucleic acid that has altered gene expression in surrogate cells from a test subject when compared to surrogate cells from a normal subject or subjects, and then comparing the genomic sequence of the nucleic acid, to identify the sequence change. In a further aspect, this nucleic acid may be found to map within the human genome within or close to or adjacent to a region that has been previously identified in a linkage study or genome scan, or associated with the disease, disorder or physical state. In yet another embodiments the present invention provides for a method of treating a disease, disorder or physical state, comprising administering a normal counterpart of a nucleic acid found to have a sequence change using methods described in this invention, including but not limited to gene therapy with nucleic acid transcripts, antisense mRNA, or other inhibitory RNAs.  
      According to the invention, the physical state can be a disease or disorder such as the presence of cancer, a neurological disorder, or a psychiatric or mood disorder, or other diseases, disorders or physical states. In specific embodiments exemplified infra, the physical state is prostate cancer, breast cancer, schizophrenia, bipolar disorder, or Alzheimer&#39;s disease. Naturally, the subject can be any multi-celled organism that can offer surrogate cells (as hereinafter defined); the examples demonstrate these methods in humans.  
      The surrogate cells can be, but are not limited to, peripheral blood leukocytes, such as monocytes, macrophages, lymphocytes, granulocytes, eosinophils neutrophils, and basophils, or other white blood cell types or subtypes. They can also be mucosal epithelia, skin, hair follicle, or CSF cells (which are predominantly leukocytes).  
      Various types of physical state evaluations can be made in accordance with the invention. For example, evaluating a physical state can involve diagnosing the presence of a disease or disorder, determining the prognosis of the subject, determining susceptibility of a subject for a disease or disorder, monitoring a therapy for a disease or disorder, developing or selecting a therapy for a disease or disorder, or classifying a disease or disorder.  
      Although the robust methods of the invention do not require it, the methods envision further testing for a biochemical marker of the physical state in the blood or some other tissue sample, or evaluating a biopsy tissue sample for the presence of the physical state.  
      The expression profiling can be accomplished using any technology to measure nucleic acid transcript levels. For example, the method could employ a nucleic acid microarray, such as an oligonucleotide microarray or a cDNA microarray. Alternatively, one could simply employ reverse transcriptase-polymerase chain reaction (RT-PCR) or Northern blot hybridization. Additional methods that could be employed include, but are not limited to, Serial Analysis of Gene Expression (SAGE), high performance liquid chromatography (HPLC), mass spectrometry, differential display, quantitative measures of allelic specific expression, Taqman assays, Molecular Beacon assays, and phage display. 
    
    
     DESCRIPTION OF THE DRAWINGS  
       FIG. 1 . TreeView Representation of Cluster patterns of gene expression among men with prostate cancer and age-matched control subjects. 1A. Data are represented in matrix format. Each row represents a single gene (for space gene names have been omitted). Each column represents an experimental leukocyte patient or control sample. For each sample the ratio of the abundance of transcripts of each gene, to the median abundance of the genes&#39;s transcript among the individuals leukocytes, is represented by a rectangle in the corresponding matrix. The rectangles each represent the magnitude of the ratio relative to the median for the total set of samples. The dendrogram along the horizontal axis indicates the clusters of most similar subjects, based on gene expression levels of 1535 genes. The dendrogram along the vertical axis represents sample nodes of the total Cluster results, where genes appear together on the branches of the tree if they have similar patterns of gene expression. Example of Cluster nodes are taken from the total TreeView data, showing genes that are generally expressed at lower levels in the prostate cancer samples (A1 to A13), than control subject samples (B1 to B7). 1B. A scaled representation of the horizontal dendrogram showing patient and control cluster results is shown.  
       FIG. 2A -B. TreeView representation of Cluster patterns of actual and randomized expression levels of 1535 genes. Relationships among samples are represented by a dendrogram “tree”, where branch lengths reflect the degree of similarity, such that short branch lengths between nodes indicate similarity between samples. The arrows indicate the direction of subject divergence along the branches from each node.  
       FIG. 3 . Partial TreeView Representation of Cluster patterns of gene expression among SZ men and control subjects. 3A Scaled representation of the horizontal dendrogram showing patient and control cluster results, based on the expression levels of 948 genes. Control Samples (C-401, 492, 536, 634 and 641) cluster into one node, SZ samples (P-493, 494, 495, 535, 588, 630, 631 and 964 (non-medicated subject)) cluster into a separate node. The sub-clusters within the SZ group do not seem to represent drug profiles, and the non-medicated subject (P-964) clusters within the SZ cluster node. The rectangles beneath each subject number represent the average signal intensity of a sample node of genes down regulated in SZ subjects.  
       FIG. 4 . TreeView Representations of Cluster patterns of gene expression among SZ and BPD subjects. Data are represented in matrix format. Each row represents a single gene (for space gene names have been omitted). Each column represents an experimental leukocyte sample. For each sample the ratio of the abundance of transcripts of each gene, to the median abundance of the genes&#39;s transcript among the individuals leukocytes, is represented a rectangle in the corresponding matrix. The rectangles each represent the magnitude of the ratio relative to the median for the total set of samples. The dendrogram along the horizontal axis indicates the clusters of most similar subjects, based on gene expression levels of 1002 genes. The dendrogram along the vertical axis represents nodes, where genes appear together on the branches of the tree if they have similar patterns of gene expression. 4A. Example of Cluster nodes taken from the total TreeView data, showing genes that are expressed at lower levels (green) or absent (grey) in the SZ patients (SZ-493, 494, 495, 535, 588, 630, 631, and 964 (non-medicated), than the leukocyte samples taken from men with BPD (BPD-767, 846). 4B. A scaled representation of the horizontal dendrogram showing subject cluster results.  
       FIG. 5 . TreeView representation of Cluster patterns of actual and randomized expression levels of 1002 genes. Relationships among samples are represented by a dendrogram “tree”, where branch lengths reflect the degree of similarity, such that short branch lengths between nodes indicate similarity between samples. The arrows indicate the direction of subject divergence along the branches from each node. 5A. A scaled representation of the horizontal dendrogram described in  FIG. 4 , where BPD subjects (BPD-747, and 846) cluster in one sub-node. 5B. A scaled representation of the TreeView readout generated when the gene expression levels of 1002 genes were randomized for each subject. Short branch length between nodes (in comparison to those observed in 5A) suggests only minor differences between samples.  
       FIG. 6 .—The proportion of top ranked genes/ESTs that map to regions of schizophrenia linkage, filtered by increasing expression level cutoffs. Genes/ESTs were sorted by t-test p value (lowest to highest). The dataset was then subjected to a filtering step using increasing stringency in the form of signal intensity cutoffs (20 intensity unit steps). For each intensity cutoff, genes/ESTs that did not have 2 or more subjects with expression levels 2 the cutoff value were removed, and the number of genes/ESTs that map to regions of schizophrenia linkage within the top 10 of all genes/ESTs that passed the filters, were then plotted on the Y axis for each intensity cutoff level (X-axis). Filled grey circles indicate the sum total of linked genes/ESTs for each intensity cutoff. Thirty sets of randomized linkage data were also analyzed at each intensity cutoff point, and are shown by the filled black circles. 
    
    
     DETAILED DESCRIPTION  
      The present invention provides novel “gene signatures” that are indicative of a physical state, e.g., a disease or disorder of a subject. These gene signatures, or expression profiles, are obtained from surrogate cells, such as blood cells, mucosal epithelial cells, and the like, that are available through non-invasive or minimally invasive procedures. Using the power of informative multiple gene expression profiling, or alternatively the coupling of multiple single gene expression measurements, the expression profile as described in the present invention permits the accurate classification, diagnosis, staging, and prognosis of diseases, determination of a biological, psychiatric, neurological or physical state including aging. The present invention also permits the prediction and evaluation of efficacy of therapeutic and treatment regimens and monitoring of subjects, and evaluation of candidates compounds for development and/or use as therapeutics. This invention also allows for the identification of candidate nucleic acids involved in the etiology and or susceptibility for a physical state.  
      This invention has significant advantages over current diagnostic and prognostic technologies. It does not require highly invasive techniques, such as tumor biopsy, that are required for confirming diagnosis of a cancer or other tissue conditions. Furthermore, it provides a biological measurement that permits a more conclusive diagnosis of diseases and conditions that are presently only conditionally diagnosed with conflation available only upon post-mortem examination, such as Alzheimer&#39;s disease, or for which no specific biological markers may be available, such as schizophrenia. In addition, this approach for discovery and validation of candidate genes for a physical state, utilizes a surrogate tissue, and therefore expands diagnostic choice and does not depend on the ability to access postmortem brain tissue, biopsied tumor tissue, or other involved tissues through invasive procedures. Indeed, invasive mechanisms of collection can greatly effect downstream gene expression, leading to great variability and inconsistencies between samples. The present invention is based, in part, on experiments which gave a complete classification of peripheral leukocyte expression clusters of prostate cancer patients (irrespective of race) when compared to age-matched normal controls, and a classification into expression clusters for schizophrenia and bipolar disorder patients compared to age- and race-matched controls (in this case with no significant effect of drug treatment for the schizophrenia on the expression profiles). Furthermore, the expression clusters of the schizophrenia subjects were distinct from those of the bipolar subjects.  
      In particular, for both prostate cancer and the psychiatric conditions, specific patterns, or signatures, of leukocyte gene expression that can both distinguish between control subjects and patients, and also differentiate between different psychiatric illnesses, have been identified.  
      Experiments showing the accurate classification of prostate cancer patients and healthy control subjects into their respective groups, based on the expression levels of over 1500 genes, support breast cancer diagnosis though leukocyte expression signatures. Specifically, while the genes employed above for classification of prostate cancer will not necessarily be the exact genes employed for classification of breast cancer, common similarities between breast and prostate cancer, including incidence and mortality rates, risk factors, initiation of transformation, and roles of androgens and estrogens (reviewed in Lopez-Otin &amp; Diamandis 1998; Coffey S. 2001; Cavalieri &amp; Rogan. 2002; Liao et al., 2002; Grover &amp; Martin 2002) indicate that growth and development of a breast cancer will exert an effecton the immune system, similar to that predicted for prostate cancer, that can be detected at the level of altered gene expression in peripheral blood leukocytes.  
      It seems clear that the use of multiple nucleic acid transcripts for the determination of expression signatures provides considerably more detailed information on disease stage and prognosis than can be provided by the quantitation of individual serum protein levels, as described in the Background to the Invention. It should also be noted that although surrogate cell gene expression levels will be measured, if, e.g., malignant breast cells were also present in the blood of patients, then gene expression of these cells will also be quantified. It seems likely that the detection of gene expression in affected cells within blood might actually increase the specificity of the analysis, as mRNA levels arising from circulating involved cells would differ from mRNA levels in prostate cancer patients with no such cells in their blood stream, and to a even greater degree than normal control subjects.  
      These results form the basis of a diagnostic screen. A clinical assay would initially involve extraction of a surrogate tissue, such as a blood sample, from the subject at risk for the condition to be tested. A labeled probe synthesized from RNA extracted from the surrogate cells can be hybridized to a microarray containing a number of genes (determined according to this invention) that are differentially expressed between patients and control individuals to identify whether the test subject has the particular condition. The resultant expression pattern can then be compared to a set of known multigene signatures that more specifically characterize the condition, e.g., expression profiles that are specific for individual stages of tumor progression. The invention represents a non-invasive diagnostic assay that can yield both diagnostic and staging information for each individual at risk.  
      Since this assay will measure gene expression within surrogate cells such as leukocytes, instead of cells directly involved in the physical state, and does not rely on the measurement of biomolecules secreted from involved cells, the resultant assay is sensitive and accurate, and capable of detecting conditions that are still at an early stage. Such an assay serves as an important pre-screen that can, with a minimum of patient discomfort, identify subjects who have the particular condition.  
     Definitions  
     Specialized  
      As used herein, the term “physical state” refers to the physiological, psychological, and health status of a subject. Various physical states include diseases and disorders, such as: proliferative disorders including cancer; pulmonary disorders; dermatological diseases; developmental disorders; muscular disorders; respiratory diseases; sexual, fertility and gynecological disorders; allergic disorders; inflammatory disorders (e.g. ulcerative colitis etc.); infectious diseases; parasitic infestations; growth abnormalities, a hyperactive or hypoactive endocrine syndrome (e.g., hyperthyroidism, hypothyroidism, growth hormone deficiency or dwarfism, type I diabetes, type II diabetes, etc.); neurological diseases (e.g., Alzheimer&#39;s, Parkinson&#39;s, Huntington&#39;s, ALS, etc.); psychiatric and mood disorders (e.g., schizophrenia, bipolar disorder, depression, obsessive-compulsive disorder, etc.); obesity; sleep disorders; other pathological conditions; and normal and abnormal aging. Physical states also include altered metabolic states, which may be due to ingestion of exposure to, pharmaceuticals, chemicals, alcohol, environmental toxins, food toxins, and the like; metabolic or nutritional conditions or deficiencies, such as but not limited to hyperlipidemia, hypercholesterolemia, malnutrition, and vitamin deficiencies. The data show a possible hierarchy of effects: a disease like schizophrenia seems to have greater impact on expression profiles of blood cells than the neuroleptic drugs that the schizophrenic patients are taking for the condition. A normal physiological state is a special kind of physical state, which can be determined from the methods of the invention.  
      The term “expression profile” refers to expression of two or more, preferably three or more, for example 5, 10, 20, 50, 100, 500, or 1000 or more, genes/EST or other transcribed nucleic acids. Genes/ESTs or nucleic acids within a subject&#39;s expression profile can be expressed at different levels (either to a greater or lesser extent, e.g., by about 2-fold of more, or less than 2-fold, and preferably within the error limits of the detection) to the gene expression profile levels of a subject or subjects with a physical state, and also for example, between subjects treated with therapeutic compounds, or between treated and untreated subjects. The differences between subjects expression profiles can then for example, be employed for diagnosing the presence of a physical state, determining the prognosis of the subject, determining susceptibility of a subject for a physical state, monitoring a therapy for a physical state, developing or selecting a therapy for a physical state, or classifying a physical state. In certain embodiments, genes in an expression profile may not include known markers of the involved cells, e.g., PSA in prostate cancer (given the highly sensitive detection technologies available, efforts are made to detect cancer cell genes in the low population of circulating metastatic cells), but in early stage non-disseminated disease such markers may well be expressed in the surrogate cells and be informative. The expression profile is indicative of a particular physical state. As used herein, the expression profile of a gene is preferably the level of mRNA, e.g., measured using microarrays or RT-PCR as described herein. In particular embodiments, nucleic acids (e.g., mRNA) expressed by a cell are reverse transcribed into either cDNA or cRNA, and the abundances of the cDNA and/or cRNA molecules are measured. Expression profiles can be presented in various forms, as discussed below, including through dendograms, TreeView readouts, color matrixes, charts, graphs, or by computer analysis without visualization. Determination of expression profiles involves analyzing expression of genes in subjects diagnosed, for example using statistical analyses, or hierarchical clustering or classification algorithms (with as much accuracy and precision as possible, including through post-mortem confirmation if necessary) with the particular physical state.  
      As used herein, the term “surrogate cells” refers to cells from a tissue source that is not the primary involved tissue of the physical state of the subject (except of course to the extent that “normal” is a special type of physical state, then the surrogate cells exhibit “normal” expression patterns). The term includes but need not be limited to blood cells, mucosal epithelial cells, skin cells, cells of hair follicles, cells from cerebrospinal fluid (CSF), and cells from lymphatic fluid. One of the advantages of the invention lies in the power to analyze expression patterns from complex mixtures of cells that might be present in any given tissue source, as discussed in the Examples. Thus, blood cells include leukocytes (monocytes, macrophages, lymphocytes, granulocytes, eosinophils, etc.), as well as platelets and megakaryocytes. Skin cells include Langerhans cells, keratinocytes, and dermal cells. Furthermore, the surrogate cells can be purified populations or subpopulations of these cells, e.g., T or B lymphocytes separated from the blood cells. However, this is not necessary for practicing the invention.  
      Surrogate cells are predominantly not the cells affected by the physical state (except, of course, for a normal physical state or normal aging) but the term does not exclude the possibility that disease cells are present in the surrogate cells. Thus, if the disease is cancer and the surrogate cells are blood cells, there may be some metastatic cells in the blood cells. However, tumor cells from a biopsy would clearly not be surrogate cells for purposes of this invention. Furthermore, purification of involved cells is not necessary, and falls outside the definition of surrogate cells.  
      The term “subject” can mean patient, test subject, animal including laboratory animals, or any entity capable of testing for physical state by obtaining an expression profile or signature of surrogate cells, including plants, for example, a genetically modified plant species. Preferably a patient is a human, but can also be a domestic animal or pet (e.g., a dog, cat, etc.), a farm animal (e.g., horse, cow, sheep, pig, goat, etc.), or a wild animal, such as in a zoo. A test subject can be a human or animal involved in a clinical trial of a drug or in a trial, as exemplified herein, for determining new, expanded, or refined expression profiles. Clearly the groups of “patients” and “test subjects” can overlap. Laboratory animals include mice, rats, rabbits, hamsters, cats, dogs, etc.  
      The term “genetically linked” refers to the proximity of two or more genes and/or traits within the genome of an organism that causes those genes or traits to be inherited, transferred, or moved together with a frequency greater than for genes or traits not linked. The linkage is a continuous variable and is inversely related to the distance between genes/traits on the genome. For investigating linkage of diseases, disorders or physical states, such as schizophrenia, genetic linkage is measured by the heritability within a family (and families) of genes or markers of interest, whereby genes or markers within a particular chromosome location are linked to a disease, disorder or physical state if allelic variation of the gene or marker segregates within the family with the disease, disorder or physical state. Those genomic regions are considered likely to contain genes which, when mutated or altered or deleted, contribute to susceptibility, or the cause or pathogenesis or etiology of a disease, disorder or physical state. For example, for schizophrenia linkage has been suggested for multiple genomic regions including chromosomes 1q23.3-q31.1, 2 p12-q22.1, 3p25.3-p22.1, 5q23.2-q34, 11q22.3-24.1, 6pter-p22.3, 2q22.1-q23.3, 1p13.3-q23.3, 8p22-p21.1, 6q15-q23.2, 6p22.3-p21.1, 10pter-p14, 14pter-q13.1, 15q21.3-q26.1, 16 p13-q12.2, 17q21.33-q24.3, 18q22.1-qter, 20 p12.3-p11, 22pter-q12.3 (Lewis et al., Am J Hum Genet. 2003; 73(1):34-48) According to one embodiment of the presently claimed methods, nucleic acids representing genes or ESTs that have a different expression profiles in surrogate cells from a subject having or suspected of having a physical state compared with cells from normal individuals not having a physical state, which can also be linked to that disease, disorder or physical state, will be chosen for genetic mutation analysis, i.e., by sequencing. As used herein, the term genetically linked also includes nucleic acid sequences representing genes or ESTs on chromosomal regions that are proximal or distal to the linked site.  
      In a specific embodiment, exemplified below, one can identify relevant genes whose expression is up- or down-regulated in disease conditions such as prostate cancer or disorders such as schizophrenia. For further diagnosis and testing, one can prepare arrays with all or a subset of all of the genes. For example, such an array employs a probe for at least one such gene, preferably at least 5, more preferably at least 10, more preferably at least 50, and more preferably at least 100, or 500, or 1000 or more such genes. Furthermore, genes are selected for inclusion in an array on the basis of the significance level of the differential expression. A significance level of less p&lt;0.1 (e.g., using the Student&#39;s two-tailed test) indicates a trend towards significance; a significance level of p&lt;0.05 provides greater certainty; a significance level of p&lt;0.01 even greater certainty. It should be understood that the value of p may change with greater sample size.  
      Thus, in one embodiment, one can diagnose the presence of prostate cancer using expression data for one or more, preferably 5 or more, more preferably 10, 50, or 100 or more genes from Table 1, below. Preferably, the genes are selected as having a trend level of p&lt;0.1, or more preferably a significance level of p&lt;0.05, and more preferably p&lt;0.01. In one embodiment, the gene probe on the expression array detects one or more of proteasome (prosome, macropain) subunit, alpha type, 5; S-phase kinase-associated protein 1A (p19A); KIAA0542 gene product; endothelial differentiation, G-protein-coupled receptor 6; tubulin, alpha 1 (testis specific); chromosome 10 open reading frame 6; G-rich RNA sequence binding factor 1; Rab acceptor 1 (prenylated); solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 7; cAMP responsive element modulator; Wiskott-Aldrich syndrome (eczema-thrombocytopenia); glutamate receptor, metabotropic 4; dynamin 2; glycosyltransferase AD-017; dimethylarginine dimethylaminohydrolase 2; similar to transcription factor TBX10; Tubulin, Alpha 1, Isoform 44; pyruvate kinase, muscle; splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor); ubiquitin-activating enzyme E1 (A1S9T and BN75 temperature sensitivity complementing); huntingtin-associated protein 1 (neuroan 1); ubiquitin ligase E3 alpha-II; ubiquitin-conjugating enzyme E2N (UBC13 homolog, yeast); potassium voltage-gated channel, shaker-related subfamily, beta member 2; farnesyltransferase, CAAX box, alpha; ATPase, H+ transporting, lysosomal 16 kDa, V0 subunit c; eukaryotic translation initiation factor 2B, subunit 4 delta, 67 kDa; and likely ortholog of mouse variant polyadenylation protein CSTF-64. In another embodiment, an expression array of the invention can include any genes with a significance of e.g. p&lt;0.0005, or alternatively with a significance of p&lt;0.001, or a trend level of significance of p&lt;0.07, from Table 1.  
      Thus, in one embodiment, one can diagnose the presence of schizophrenia using expression data for one or more, preferably 5 or more, more preferably 10, 50, or 100 or more genes from Table 2, below. Preferably, the genes are selected as having a trend level of p&lt;0.1, or more preferably a significance of p&lt;0.05, and more preferably p&lt;0.01. In one embodiment, the gene probe on the expression array detects one or more of par-6 partitioning defective 6 homolog alpha ( C. elegans ) (also called  homo sapiens  tax interaction protein 40), transmembrane 4 superfamily member tetraspan NET-5, neural cell adhesion molecule 1, cadherin 16, KSP-cadherin WD repeat domain 1, growth hormone releasing hormone B-cell translocation gene 1, anti-proliferative solute carrier family 10 (sodium/bile acid cotransporter family), and member 1 HRIHFB2206 protein. In another embodiment, an expression array of the invention can include any genes with a significance of e.g. p&lt;0.0005, or alternatively with a significance of p&lt;0.001, or a trend level of significance of p&lt;0.07, from Table 2.  
     Generalized  
      The terms used in this specification generally have their ordinary meanings in the art, within the context of this invention and in the specific context where each term is used. Certain terms are discussed below, or elsewhere in the specification, to provide additional guidance to the practitioner in describing the compositions and methods of the invention and how to make and use them.  
      As used herein, the term “isolated” means that the referenced material is removed from the environment in which it is normally found. Thus, an isolated biological material can be free of cellular components, i.e., components of the cells in which the material is found or produced. In the case of nucleic acid molecules, an isolated nucleic acid includes isolated DNA, a PCR product, isolated RNA (mRNA, cRNA, tRNA, rRNA), a cDNA, or a restriction fragment. In another embodiment, an isolated nucleic acid is preferably excised from the chromosome in which it may be found, and more preferably is no longer joined to non-regulatory, non-coding regions, or to other genes, located upstream or downstream of the gene contained by the isolated nucleic acid molecule when found in the chromosome. In yet another embodiment, the isolated nucleic acid lacks one or more introns. Isolated nucleic acid molecules include sequences inserted into plasmids, cosmids, artificial chromosomes, and the like. Thus, in a specific embodiment, a recombinant nucleic acid is an isolated nucleic acid. An isolated protein may be associated with other proteins or nucleic acids, or both, with which it associates in the cell, or with cellular membranes if it is a membrane-associated protein. An isolated organelle, cell, or tissue is removed from the anatomical site in which it is found in an organism. An isolated material may be, but need not be, purified.  
      The term “purified” as used herein refers to material that has been isolated under conditions that reduce or eliminate the presence of unrelated materials, i.e., contaminants, including native materials from which the material is obtained. For example, a purified nucleic acid molecule is preferably substantially free of proteins or other unrelated nucleic acid molecules with which it can be found within a cell. As used herein, the term “substantially free” is used operationally, in the context of analytical testing of the material. Preferably, purified material substantially free of contaminants is at least 50% pure; more preferably, at least 90% pure, and more preferably still at least 99% pure. Purity can be evaluated by chromatography, gel electrophoresis, immunoassay, composition analysis, biological assay, mass spectrometry and other methods known in the art.  
      Methods for purification are well known in the art. For example, nucleic acids can be purified by precipitation, chromatography (including preparative solid phase chromatography, oligonucleotide hybridization, and triple helix chromatography), ultracentrifugation, and other means. A purified material may contain less than about 50%, preferably less than about 75%, and most preferably less than about 90%, of the cellular components with which it was originally associated. The “substantially pure” indicates the highest degree of purity which can be achieved using conventional purification techniques known in the art.  
      A “sample” as used herein refers to a biological material which can be tested, e.g., a tissue, for example a surrogate tissue, comprising cells, that are tested or analyzed for the presence or absence of certain particular nucleic acid sequences, corresponding to certain genes that may be expressed by the cell or present in the cell.  
      A “gene” is a sequence of nucleotides which code for a functional “gene product”. Generally, a gene product is a functional protein. However, a gene product can also be another type of molecule in a cell, such as an RNA. For the purposes of the present invention, a gene product also refers to an mRNA sequence which may be found in a cell. For example, measuring gene expression levels according to the invention may correspond to measuring mRNA levels.  
      The term “express” and “expression” means allowing or causing the information in a gene or DNA sequence to become manifest, for example producing RNA (such as mRNA) or a protein by activating the cellular functions involved in transcription and translation of a corresponding gene or DNA sequence. A DNA sequence is expressed by a cell to form an “expression product” such as an RNA (e.g., an mRNA) or a protein. The expression product itself, e.g., the resulting RNA or protein, may also said to be “expressed” by the cell. As used herein, the term expression also refers to the amount or abundance of mRNA corresponding to a particular gene that is present in a cell.  
      “Amplification” of a nucleic acid, as used herein, denotes the use of an amplification synthetic process, such as polymerase chain reaction (PCR), to increase the concentration of a particular DNA or cDNA, or mRNA or cRNA sequence within a mixture of nucleic acid sequences. For a description of PCR see Saiki et al., Science 1988, 239:487.  
      The term “inhibitory RNA” can refer to an RNA species that can directly or indirectly inhibit expression of a gene or other nucleic acids by interfering with, or decreasing the process of transcription, and/or directly or indirectly increasing the degradation or cleavage of the targeted gene or nucleotide transcript, thus reducing the gene or nucleic acid&#39;s transcript levels or expression levels at the RNA and/or protein level. RNA molecules can be used to cause inhibition of expression of genes or other nucleotide sequences. RNA molecules utilized or employed for inhibition, can contain in whole or part, sequence that is at least similar to, or substantially identical to, or substantially complementary to (in whole or part), an RNA sequence produced from a gene or other nucleotide sequence being targeted (Shuey et al. Drug Discov Today. 2002 7(20):1040-6). Sequence-specific, or partically sequence specific inhibition of a gene or nucleotide transcript&#39;s expression, can be induced using several different methodologies and molecule types, including but not limited to: chemically modified antisense oligodeoxyribonucleic acids (ODNs), ribozymes and siRNAs, peptide nucleic acids (PNAs), morpholino phosphorodiamidates, DNAzymes and 5′-end-mutated U1 small nuclear RNAs (Dorsett et al. Nat Rev Drug Discov. 2004 3(4):318-29). Additionally, the introduction of single or double stranded RNA or RNA-like molecules that are preferably less than 30 nucleotides in length may be more useful for decreasing cell death and/or activation when the sequences are introduced. (Xu et al., Biochem Biophys Res Commun. 2004 316(3):680-7). The use of interference technologies such as RNAi for therapeutic approaches to physical states, diseases or disorders, can also include the introduction to cells, organs, tissues or organisms, of specific RNA molecules, either as uncomplexed oligonucleotides, and/or using viral or retroviral vectors, or other vectors such as plasmids or liposomes, containing small interfering RNA sequence (siRNA) or small hairpin RNA sequence (shRNA) or their precursor vector sequences (reviewed in Devroe et al., Expert Opin Biol Ther. 2004 4(3):319-27; Davidson et al., Lancet Neurol. 2004 (3):145-9).  
      A nucleic acid molecule is “hybridizable” to another nucleic acid molecule, such as a cDNA, oligo-DNA, or RNA, when a single stranded form of the nucleic acid molecule can anneal to the other nucleic acid molecule under the appropriate conditions of temperature and solution ionic strength (see Sambrook et al., supra). The conditions of temperature and ionic strength determine the “stringency” of the hybridization. For preliminary screening for homologous nucleic acids, low stringency hybridization conditions, corresponding to a Tm (melting temperature) of 55° C., can be used, e.g., 5×SSC, 0.1% SDS, 0.25% milk, and no formamide; or 30% formamide, 5×SSC, 0.5% SDS). Moderate stringency hybridization conditions correspond to a higher Tm, e.g., 40% formamide, with 5× or 6×SCC. High stringency hybridization conditions correspond to the highest Tm, e.g., 50% formamide, 5× or 6×SCC. SCC is a 0.15M NaCl, 0.015M Na citrate. Hybridization requires that the two nucleic acids contain complementary sequences, although depending on the stringency of the hybridization, mismatches between bases are possible. The appropriate stringency for hybridizing nucleic acids depends on the length of the nucleic acids and the degree of complementation, variables well known in the art. The greater the degree of similarity or homology between two nucleotide sequences, the greater the value of Tm for hybrids of nucleic acids having those sequences. The relative stability (corresponding to higher Tm) of nucleic acid hybridizations decreases in the following order: RNA:RNA, DNA:RNA, DNA:DNA. For hybrids of greater than 100 nucleotides in length, equations for calculating Tm have been derived (see Sambrook et al., supra, 9.50-9.51). For hybridization with shorter nucleic acids, i.e., oligonucleotides, the position of mismatches becomes more important, and the length of the oligonucleotide determines its specificity (see Sambrook et al., supra, 11.7-11.8). A minimum length for a hybridizable nucleic acid is at least about 10 nucleotides; preferably at least about 15 nucleotides; and more preferably the length is at least about 20 nucleotides.  
      Suitable hybridization conditions for oligonucleotides (e.g., for oligonucleotide probes or primers) are typically somewhat different than for full-length nucleic acids (e.g., full-length cDNA), because of the oligonucleotides&#39; lower melting temperature. Because the melting temperature of oligonucleotides will depend on the length of the oligonucleotide sequences involved, suitable hybridization temperatures will vary depending upon the oligonucleotide molecules used. Exemplary temperatures may be 37° C. (for 14-base oligonucleotides), 48° C. (for 17-base oligoncucleotides), 55° C. (for 20-base oligonucleotides) and 60° C. (for 23-base oligonucleotides). Exemplary suitable hybridization conditions for oligonucleotides include washing in 6×SSC/0.05% sodium pyrophosphate, or other conditions that afford equivalent levels of hybridization.  
      Preferably, nucleic acid molecules in the present invention are detected by hybridization to probes of a microarray. Hybridization and wash conditions are therefore preferably chosen so that the probe “specifically binds” or “specifically hybridizes” to a specific target nucleic acid. In other words, the nucleic acid probe preferably hybridizes, duplexes or binds to a target nucleic acid molecules having a complementary nucleotide sequence, but does not hybridize to a nucleic acid molecules having a non-complementary sequence. As used herein, one oligonucleotide sequence is considered complementary to another when, if the shorter of the oligonucleotides is less than or equal to about 25 bases, there are no mismatches using standard base-pairing rules, or using mismatch analysis algorithms (Affymetrix Inc). If the shorter of the two polynucleotides is longer than about 25 bases, there is preferably no more than a 5% mismatch. Preferably, the two oligonucleotides are perfectly complementary (i.e., no mismatches). It can be easily demonstrated that particular hybridization conditions are suitable for specific hybridization by carrying out the assay using negative controls. See, for example, Shalon et al., Genome Research 1996, 639-645; and Chee et al., Science 1996, 274:610-614.  
      Optimal hybridization conditions for use with microarrays will depend on the length (e.g., oligonucleotide versus polynucleotide greater than about 200 bases) and type (e.g., RNA, DNA, PNA, etc.) of probe and target nucleic acid. General parameters for specific (i.e., stringent) hybridization conditions are described above. Hybridization conditions for use of Affymetrix commercial oligonucleotide arrays have been developed for standardized use (Affymetrix Inc.) For cDNA microarrays, such as those described by Schena et al. (Proc. Natl. Acad. Sci. USA; 1996, 93:10614), typical hybridization conditions comprise hybridizing in 5×SSC and 0.2% SDS at 65° C. for about four hours, followed by washes at 25° C. in a low stringency wash buffer (for example, 1×SSC and 0.2% SDS), and about 10 minutes washing at 25° C. in a high stringency wash buffer (for example, 0.1×SSC and 0.2% SDS). Useful hybridization conditions are also provided, e.g., in Tijessen, Hybridization with Nucleic Acid Probes, Elsevier Sciences Publishers (1996), and Kricka, Nonisotopic DNA Probe Techniques, Academic Press, San Diego Calif. (1992). Generally commercially available expression screening systems that use hybridization provide defined hybridization and wash conditions.  
     Measuring Expression Profiles  
      Various commercial systems are available for profiling gene expression. These include the powerful single gene amplification processes such as reverse transcription-polymerase chain reaction (RT-PCR). Multigene profiling can be performed in single reaction mixtures using specific detection signals, such as dyes, in separate reaction mixtures, or on arrays. Various commercial systems are available for expression profiling as well.  
      eXpress Profiling (XP) by Althea (San Diego, Calif.) is useful in screening large numbers of compounds for effects on expression of a limited number of known target genes (approximately up to 20 per single well reaction). The assay employs discernible fluorescent dyes that can be reliably and simultaneously detected in a single reaction mixture. XP works by first amplifying the cDNA sources to be compared with a pair of gene-specific primers that each carry a universal sequence at their 5′ end. The resulting PCR amplicon is then further amplified with a pair of primers that hybridize to the universal sequences at both termini of the original PCR amplicon. One of the latter primer pair is fluorescently labeled, such that the final product can be quantified.  
      Assays-on-Demands by Applied Biosystems (Foster City, Calif.) can be used for validation of microarray hits. The assay provides a means of higher reliability and accuracy in the expression profiling of single genes. Each kit is custom tailored to a particular gene; kits can be combined for multigene profiles. It is useful for standardization purposes, due to better comparability of results between different experiments/laboratories. The assay uses random primers in the initial cDNA synthesis step, which enables higher quality signal detection along the transcript. The PCR amplification step is based on AB&#39;s TaqMan system which then allows one to quantify the amount of cDNA in the sample.  
      EnzyStart™ by GeneCopeia (Frederick, Md.) blocks the 3′ end of amplification primers with an enzymatically removable blocking group, which avoids non-specifically primed DNA polymerization that may otherwise occur due to primer hybridization at ambient temperature. A Terminal Blocker Group Remove Enzyme (TBGRE) present in the reaction is activated at temperatures above 55° C. to produce free hydroxyl-groups at the 3′ end of the primer, thus allowing the PCR reaction to start only after non-specifically hybridized primers are melted off the template. This is particularly useful when very low concentrations of cDNA are to be detected, when signal to noise ration is a problem.  
      Omega Beacon™ by Gorilla Genomics (Alameda, Calif.) provides a quantitative real-time PCR method useful for measurement of gene expression. These probes form stem-loop structures, where the loop sequence hybridizes specifically to the DNA target of interest. Upon hybridization the stem is destabilized and opens, which releases a fluorescence quencher from the proximity of the fluorophore, and thus allowing for fluorescence and the quantification thereof.  
      Black Hole Quenchers by Biosearch Technologies (Novato, Calif.) employs on a similar mechanism as Omega Beacons. Here fluorophore and quencher are kept in proximity in the unhybridized state due to the random coiling of the probe. Upon hybridization to the target sequence the probe is stretched out, which permits quantifiable fluorescence emission.  
     Nucleic Acid Arrays  
      The terms “array” and “microarray” are used interchangeably and refer generally to any ordered arrangement (e.g., on a surface or substrate) or different molecules, referred to herein as “probes”. Each different probe of an array specifically recognizes and/or binds to a particular molecule, which is referred to herein as its “target”. Microarrays are therefore useful for simultaneously detecting the presence or absence of a plurality of different target molecules, e.g., in a sample. In preferred embodiments, arrays used in the present invention are “addressable arrays” where each different probe is associated with a particular “address”. For example, in preferred embodiments where the probes of are immobilized on a surface or a substrate, each different probe of the addressable array may be immobilized at a particular, known location on the surface or substrate. The presence or absence of that probe&#39;s target molecule in a sample may therefore be readily determined by simply determining whether a target has bound to that particular location on the surface or substrate.  
      The methods of the invention may be practiced using nucleic acid arrays (also referred to herein as “transcript arrays” or “hybridization arrays”) that comprise a plurality of nucleic acid probes immobilized on a surface or substrate. The different nucleic acid probes are complementary to, and therefore hybridize to, different target nucleic acid molecules, e.g., in a sample. Thus such probes may be used to simultaneously detect the presence and/or abundance of a plurality of different nucleic acid molecules in a sample, including the expression of a plurality of different genes; e.g., the presence and/or abundance of different tiRNA molecules, or of nucleic acid molecules derived therefrom (for example, cDNA or cRNA).  
      There are two major types of microarray technology; spotted cDNA arrays and manufactured oligonucleotide arrays. Examples 1 and 2 employ high density oligonucleotide Affymetrix® GeneChip arrays (reviewed in Schena at el., 1998).  
      Transcript Arrays Generally. In a preferred embodiment the present invention makes use of “transcript arrays” (also called herein “microarrays”) for determining the effect of a test compound on gene expression. Transcript arrays can be employed for analyzing the transcriptional state in a surrogate cell in comparison to a known cell (whether known to be normal or known to be from a subject with an abnormal physical state).  
      Microarrays can be made in a number of ways, of which several are described below. However produced, microarrays share certain characteristics. The arrays are preferably reproducible, allowing multiple copies of a given array to be produced and easily compared with each other. Preferably the microarrays are small, usually smaller than 5 cm2, and they are made from materials that are stable under binding (e.g., nucleic acid hybridization) conditions. A given binding site or unique set of binding sites in the microarray will specifically bind the product of a single gene in the cell. Although there may be more than one physical binding site (hereinafter “site”) per specific mRNA, for the sake of clarity the discussion below will assume that there is a single site. It will be appreciated that when cDNA complementary to the RNA of a cell is made and hybridized to a microarray under suitable hybridization conditions, the level of hybridization to the site in the array corresponding to any particular gene will reflect the prevalence in the cell of mRNA transcribed from that gene. For example, when detectably labeled (with a fluorophore) cDNA complementary to the total cellular mRNA is hybridized to a microarray, the site on the array corresponding to a gene (i.e., capable of specifically binding a nucleic acid product of the gene) that is not transcribed in the cell will have little or no signal, and a gene for which the encoded mRNA is prevalent will have a relatively strong signal.  
      The use of a two-color fluorescence labeling and detection scheme to define alterations in gene expression has been described (e.g., Shena et al., Science 1995, 270:467-470). An advantage of using cDNA labeled with two different fluorophores is that a direct and internally controlled comparison of the mRNA levels corresponding to each arrayed gene in two cell states can be made, and variations due to minor differences in experimental conditions (e.g., hybridization conditions) will not affect subsequent analyses. However, it will be recognized that it is also possible to use cDNA from a single cell, and compare, for example, the absolute amount of a particular mRNA in, e.g., a treated and untreated cell.  
      By way of example, GeneChip expression analysis (Affymetrix, Santa Clara, Calif.) generates data for the assessment of gene expression profiles and other biological assays. Oligonucleotide expression arrays simultaneously and quantitatively interrogate thousands of mRNA transcripts (genes or ESTs, via a cRNA synthesis step), simplifying large genomic studies. Each transcript can be represented on a probe array by multiple probe pairs, representing different regions of the genes or ESTs, to differentiate among closely related members of gene families. Each probe cell contains millions of copies of a specific oligonucleotide probe, permitting the accurate and sensitive detection of low-intensity mRNA hybridization patterns. After hybridization intensity data is captured, e.g., using a Hewlett-Packard GeneArray™ scanner, software can be used to automatically calculate intensity values for each probe cell. Probe cell intensities can be used to calculate an average intensity for each gene, which directly correlates with mRNA abundance levels. Expression data can be quickly sorted on any analysis parameter and displayed in a variety of graphical formats for any selected subset of genes. Other gene expression detection technologies include the research products manufactured and sold by Perkin-Elmer and Gene Logic. Additionally, software such as BRB Array Tools (NCI), GeneSpring (Silicon Genetics), GeneLinker Platinum (Predictive Patterns Software Inc.) can also be used to perform clustering, gene profiling, sample classification and statistical analyses of expression profiles.  
      Preparation of Microarrays. Microarrays are known in the art and preferably comprise a surface to which short or long oligonucleotide or cDNA probes, that correspond in sequence to gene products (e.g., cDNAs, mRNAs, cRNAs, polypeptides, and fragments thereof), can be specifically hybridized or bound at a known position within the microarray. In one embodiment, the microarray is an array in which each position represents a discrete binding site for a product encoded by a gene (e.g., a protein or RNA), and in which binding sites are present for products of most or almost all of the genes in the organism&#39;s genome. In a preferred embodiment, the “binding site” (hereinafter, “site”) is a nucleic acid or nucleic acid analogue to which a particular cognate cDNA or cRNA can specifically hybridize. The nucleic acid or analogue of the binding site can be, e.g., a synthetic oligomer, a full-length cDNA, a less-than full length cDNA, or a gene fragment.  
      Although in a preferred embodiment the microarray contains binding sites for products of all or almost all genes in the target organism&#39;s genome, such comprehensiveness is not necessarily required for diagnostic arrays with a defined set of genes that are differentially expressed (the expression profile genes).  
      Preparing Nucleic Acids for Microarrays. As noted above, the “binding site” to which a particular cognate cDNA or cRNA specifically hybridizes is usually a nucleic acid or nucleic acid analogue attached at that binding site. In one embodiment, the binding sites of the microarray are DNA polynucleotides corresponding to at least a portion of each gene in an organism&#39;s genome. These DNAs can be obtained by, e.g., polymerase chain reaction (PCR) amplification of gene segments from genomic DNA, cDNA (e.g., by RT-PCR), or cloned sequences. PCR primers are chosen, based on the known sequence of the genes or cDNA, that result in amplification of unique fragments (i.e., fragments that do not share more than 10 bases of contiguous identical sequence with any other fragment on the microarray). Computer programs are useful in the design of primers with the required specificity and optimal amplification properties. See, e.g., Oligo version 5.0 (National Biosciences). In the case of binding sites corresponding to very long genes, it will sometimes be desirable to amplify segments near the 3′ end of the gene so that when oligo-dT primed cDNA probes are hybridized to the microarray, less-than-full length probes will bind efficiently. Typically each gene fragment on the microarray will be between about 50 bp and about 2000 bp, more typically between about 100 bp and about 1000 bp, and usually between about 300 bp and about 800 bp in length. PCR methods are well known and are described, for example, in Innis et al., eds., 1990, PCR Protocols: A Guide to Methods and Applications, Academic Press Inc. San Diego, Calif. It will be apparent that computer controlled robotic systems are useful for isolating and amplifying nucleic acids.  
      An alternative means for generating the nucleic acid for the microarray is by synthesis of synthetic polynucleotides or oligonucleotides, e.g., using N-phosphonate or phosphoramidite chemistries (Froehler et al., Nucleic Acid Res. 1986, 14:5399-5407; McBride et al., Tetrahedron Lett. 1983, 24:245-248). Synthetic sequences are between about 15 and about 500 bases in length, more typically between about 20 and about 50 bases. In some embodiments, synthetic nucleic acids include non-natural bases, e.g., inosine. As noted above, nucleic acid analogues may be used as binding sites for hybridization. An example of a suitable nucleic acid analogue is peptide nucleic acid (see, for example, Egholm et al., Nature 1993, 365:566-568. See, also, U.S. Pat. No. 5,539,083).  
      In an alternative embodiment, the binding (hybridization) sites are made from plasmid or phage clones of genes, cDNAs (e.g., expressed sequence tags), or inserts therefrom (Nguyen et al., Genomics 1995, 29:207-209). In yet another embodiment, the polynucleotide of the binding sites is RNA.  
      Attaching Nucleic Acids to the Solid Surface. The nucleic acids or analogues are attached to a solid support, which may be made from glass, plastic (e.g., polypropylene, nylon), polyacrylamide, nitrocellulose, or other materials. A preferred method for attaching the nucleic acids to a surface is by printing on glass plates, as is described generally by Schena et al., Science 1995, 270:467-470. This method is especially useful for preparing microarrays of cDNA. See also DeRisi et al., Nature Genetics 1996, 14:457-460; Shalon et al., Genome Res. 1996, 6:639-645; and Schena et al., Proc. Natl. Acad. Sci. USA 1995, 93:10539-11286.  
      A second preferred method for making microarrays is by making high-density oligonucleotide arrays. Techniques are known for producing arrays containing thousands of oligonucleotides complementary to defined sequences, at defined locations on a surface using photolithographic techniques for synthesis in situ (see, Fodor et al., Science 1991, 251:767-773; Pease et al., Proc. Natl. Acad. Sci. USA 1994, 91:5022-5026; Lockhart et al., Nature Biotech. 1996, 14:1675. See, also, U.S. Pat. Nos. 5,578,832; 5,556,752; and 5,510,270) or other methods for rapid synthesis and deposition of defined oligonucleotides (Blanchard et al., Biosensors &amp; Bioelectronics 1996, 11:687-90). When these methods are used, oligonucleotides (e.g., 20-mers) of known sequence are synthesized directly on a surface such as a derivatized glass slide. Usually, the array produced is redundant, with several oligonucleotide molecules per RNA. Oligonucleotide probes can be chosen to detect alternatively spliced mRNAs.  
      Other methods for making microarrays, e.g., by masking (Maskos and Southern, Nuc. Acids Res. 1992, 20:1679-1684), may also be used. In principal, any type of array, for example, dot blots on a nylon hybridization membrane (see, Sambrook et al., Molecular Cloning—A Laboratory Manual (2nd Ed.), Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1989), could be used, although, as will be recognized by those of skill in the art, very small arrays will be preferred because hybridization volumes will be smaller.  
      Generating Labeled Probes. Methods for preparing total and poly(A)+ RNA are well known and are described generally in Sambrook et al., supra. In one embodiment, RNA is extracted from cells of the various types of interest in this invention using guanidinium thiocyanate lysis followed by CsCl centrifugation (Chirgwin et al., Biochemistry 1979, 18:5294-5299). Poly(A)+ RNA is selected by selection with oligo-dT cellulose (see Sambrook et al., supra). Cells of interest may include, but are not limited to, wild-type cells, surrogate cells, drug-exposed wild-type cells, modified cells, and drug-exposed modified cells.  
      Labeled cDNA is prepared from mRNA by oligo dT-primed or random-primed reverse transcription, both of which are well known in the art (see, for example, Klug and Berger, Methods Enzymol. 1987, 152:316-325). Reverse transcription may be carried out in the presence of a dNTP conjugated to a detectable label, most preferably a fluorescently labeled dNTP. Alternatively, isolated mRNA can be converted to labeled antisense RNA synthesized by in vitro transcription of double-stranded cDNA in the presence of labeled dNTPs (Lockhart et al., Nature Biotech. 1996, 14:1675). In alternative embodiments, the cDNA or RNA probe can be synthesized in the absence of detectable label and may be labeled subsequently, e.g., by incorporating biotinylated dNTPs or rNTP, or some similar means (e.g., photo-cross-linking a psoralen derivative of biotin to RNAs), followed by addition of labeled streptavidin (e.g., phycoerythrin-conjugated streptavidin) or the equivalent.  
      When fluorescently-labeled probes are used, many suitable fluorophores are known, including fluorescein, lissamine, phycoerythrin, rhodamine (Perkin Elmer Cetus), Cy2, Cy3, Cy3.5, Cy5, Cy5.5, Cy7, Fluor X (Amersham) and others (see, e.g., Kricka, 1992, Nonisotopic DNA Probe Techniques, Academic Press San Diego, Calif.). It will be appreciated that pairs of fluorophores are chosen that have distinct emission spectra so that they can be easily distinguished.  
      In another embodiment, a label other than a fluorescent label is used. For example, a radioactive label, or a pair of radioactive labels with distinct emission spectra, can be used (see Zhao et al., Gene 1995, 156:207; Pietu et al., Genome Res. 1996, 6:492). However, because of scattering of radioactive particles, and the consequent requirement for widely spaced binding sites, use of radioisotopes is a less-preferred embodiment.  
      In one embodiment, labeled cDNA is synthesized by incubating a mixture containing 0.5 mM dGTP, dATP and dCTP plus 0.1 mM dTTP plus fluorescent deoxyribonucleotides (e.g., 0.1 mM Rhodamine 110 UTP (Perken Elmer Cetus) or 0.1 mM Cy3 dUTP (Amersham)) with reverse transcriptase (e.g., SuperScript™ II, LTI Inc.) at 42° C. for 60 minutes.  
      Hybridization to Microarrays. Nucleic acid hybridization and wash conditions are chosen so that the probe “specifically binds” or “specifically hybridizes” to a specific array site, i.e., the probe hybridizes, duplexes or binds to a sequence array site with a complementary nucleic acid sequence but does not hybridize to a site with a non-complementary nucleic acid sequence. As used herein, one polynucleotide sequence is considered complementary to another when, if the shorter of the polynucleotides is less than or equal to 25 bases, there are no mismatches using standard base-pairing rules or, if the shorter of the polynucleotides is longer than 25 bases, there is no more than a 5% mismatch. Preferably, the polynucleotides are perfectly complementary (no mismatches). It can easily be demonstrated that specific hybridization conditions result in specific hybridization by carrying out a hybridization assay including negative controls (see, e.g., Shalon et al., supra; and Chee et al., supra).  
      Optimal hybridization conditions will depend on the length (e.g., oligomer versus polynucleotide greater than 200 bases) and type (e.g., RNA, DNA, PNA) of labeled probe and immobilized polynucleotide or oligonucleotide. General parameters for specific (i.e., stringent) hybridization conditions for nucleic acids are described above. When cDNA microarrays, such as those described by Schena et al. are used, typical hybridization conditions are hybridization in 5×SSC plus 0.2% SDS at 65 1C for 4 hours, followed by washes at 25° C. in low stringency wash buffer (e.g., 1×SSC plus 0.2% SDS) followed by 10 minutes at 25° C. in high stringency wash buffer (0.1×SSC plus 0.2% SDS). See, Shena et al., Proc. Natl. Acad. Sci. USA 1996, 93:10614). Useful hybridization conditions are also provided in, e.g., Tijessen, 1993, Hybridization With Nucleic Acid Probes, Elsevier Science Publishers B.V. See, also, Kricka, 1992, Nonisotopic DNA Probe Techniques, Academic Press, San Diego, Calif.  
      Signal Detection and Data Analysis. When fluorescently labeled probes are used, the fluorescence emissions at each site of a transcript array can be preferably detected by scanning confocal laser microscopy. In one embodiment, a separate scan, using the appropriate excitation line, is carried out for each of the two fluorophores used. Alternatively, a laser can be used that allows simultaneous specimen illumination at wavelengths specific to the two fluorophores and emissions from the two fluorophores can be analyzed simultaneously (see, Shalon et al., Genome Research 1996, 6:639-645). In a preferred embodiment, the arrays are scanned with a laser fluorescent scanner with a computer controlled X-Y stage and a microscope objective. Sequential excitation of the two fluorophores is achieved with a multi-line, mixed gas laser and the emitted light is split by wavelength and detected with two photomultiplier tubes. Fluorescence laser scanning devices are described in Schena et al., Genome Res. 1996, 6:639-645 and in other references cited herein. Alternatively, the fiber-optic bundle described by Ferguson et al., Nature Biotech. 1996, 14:1681-1684, may be used to monitor mRNA abundance levels at a large number of sites simultaneously.  
      Signals are recorded and, in a preferred embodiment, analyzed by computer, e.g., using a 12 bit analog to digital board. In one embodiment the scanned image is despeckled using a graphics program (e.g., Hijaak Graphics Suite) and then analyzed using an image gridding program that creates a spreadsheet of the average hybridization at each wavelength at each site. If necessary, an experimentally determined correction for “cross talk” (or overlap) between the channels for the two fluors may be made. For any particular hybridization site on the transcript array, a ratio of the emission of the two fluorophores can be calculated. The ratio is independent of the absolute expression level of the cognate gene, but is useful for genes whose expression is significantly modulated, e.g., by administering a drug, drug-candidate or other compound, or by any other tested event.  
      In one embodiment of the invention, the relative abundance of an mRNA in two cells or subjects or cell lines tested (e.g., in a treated verses untreated cell or subject) may be scored as perturbed (i.e., where the abundance is different in the two sources of mRNA tested) or as not perturbed (i.e., where the relative abundance in the two sources is the same or is unchanged). Preferably, the difference is scored as perturbed if the difference between the two sources of RNA of at least a factor of about 10% (i.e., RNA from one sources is about 10% more abundant than in the other source), or may be about 25% or about 50%. Still more preferably, the RNA may be scored as perturbed when the difference between the two sources of RNA is at least about a factor of 1.5. Indeed, the difference in abundance between the two sources may be by a factor of two, of five, or more.  
      In other embodiments, it may be advantageous to also determine the magnitude of the perturbation. This may be done, as noted above, by calculating the ratio of the emission of the two fluorophores used for differential labeling, or by analogous methods that will be readily apparent to those of skill in the art.  
      In a specific embodiment, exemplified below, Affymetrix® Microarray Suite software can be employed for image acquisition and normalization of the fluorescent signals using internal standards. Analysis of the resultant signal intensities over each oligonucleotide, or data point, within each experiment may then fall into two main categories: supervised learning algorithms (Golub et al., 1999; Slonim et al., 1999; Yeang et al., 2001; Ramaswamy et al., 2001), and Hierarchical Clustering (Eisen et al., 1998; Alizadeh et al., 2000; Perou et al., 2000) (see Example A for the full reference citations). Preferably any algorithms to be employed have the capacity to analyze the very large datasets, and allow comparisons of multiple experiments and multiple points within a single experiment, for determining expression profiles.  
     EXAMPLES  
      The following Example(s) illustrate the invention, but are not limiting.  
     Example 1  
     Expression Profiling of Blood Cells Distinguishes Prostate Cancer Patients  
      Patient and Control Subject Recruitment and Study Procedure Institutional Review Board (IRB) approval of the study protocol was obtained.  
      Medical Exclusions. A list of medical exclusions was generated for both prostate cancer patients and control subjects. A blood count (CBC) was performed for all samples collected and subjects were excluded if their cell counts were outside of the normal range. Serum PSA tests were performed on all patient and control subjects. Any control subject with serum PSA &gt;4 ng/ml was excluded from further analysis (n=0).  
      Prostate Cancer Subjects. Eleven subjects have been recruited for this study since the initiation of screening of men undergoing radical prostatectomy for treatment of prostate cancer. For all subjects, informed consent was obtained according to the regulations of the IRB. Subjects completed a questionnaire (with the assistance of the study coordinator), documenting current medication and general health status. Fifteen ml of blood was then drawn prior to surgery for prostate removal. Blood was processed immediately as described below. All patient records were screened and pertinent data entered into the subject database, such as serum PSA values (at the time of surgery, prior to surgery, and post surgery), date of biopsy, Gleason score at biopsy and post prostatectomy, TNM tumor stage. The IRB approved study protocol allows the study team to access all patient records following surgery. Ethnicity of prostate cancer subjects was as follows: Caucasian=5, Hispanic=3, African American=2, Asian=1.  
      Control Subjects. Seven control subjects, age-matched to the patient group, were recruited. Subjects completed a questionnaire documenting that neither they nor their first degree relatives had a history of prostate cancer, or any other tumor. Questionnaires were also completed listing current medication use and medical history. Subjects were seen at their place of work and an informed consent interview was conducted and consent obtained according to the regulations of the IRB. 15 ml blood was drawn from each control and processed immediately as described below. 3 ml blood was employed for PSA and CBC tests, 12 ml was employed for leukocyte extraction. Ethnicity of age-matched control subjects was as follows: Caucasian=4, Hispanic=2, African American=1, Asian=0.  
      Sample Processing and Microarray Hybridization. Immediately after collection, blood leukocytes were isolated by lysis of red cells, centrifugation and washing, according to standard protocols (Qiagen). Total purified leukocytes were split into two tubes and stored at −70° C. prior to RNA extraction. In studies performed for other projects it is possible to store leukocyte samples for up to 6 months with no effect to quality or quantity of the RNA extracted. Total RNA was extracted in duplicate from the two leukocytes samples, using an RNA preparation kit and accompanying protocol (Qiagen). RNA was quantified by UV spectrometry, using RNA standards for normalization. The quality of RNA was analyzed by electrophoresis through formaldehyde agarose gels. Only RNA samples with good quality ribosomal RNA were processed to completion. For samples employed for microarray analysis, 8 μg of total RNA was used as a template for cDNA synthesis, using an oligo-dT primer and Reverse Transcriptase enzyme, according to standard Affymetrix protocols. Purified cDNA was then employed as a template to generate biotin labeled cRNA, using Enzo Bioarray High Yield RNA Transcript labeling Kits (Enzo). cRNA samples were quantified and stored at −70° C. prior to fragmentation and hybridization.  
      Following fragmentation of the cRNA samples, 20 ng of each fragmented product was hybridized to an Affymetrix TEST3 array to check the quality of each sample. In each instance the cRNA sample was then hybridized to an HU95A GeneChip array. Patient and control samples were processed and hybridized in a random order.  
      Affymetrix® Microarray Suite Software. Following scanning of GeneChip arrays, data acquisition of each array was performed using the Affymetrix Microarray Software Suite V5. Briefly, this software initially quantifies the signal over every oligonucleotide probe set on the microarray, then normalizes against the intensity of the signal over the internal control oligonucleotides. The probe set for each gene is then queried by perfect match (PM) and mismatch (MM) oligonucleotide probes, each 25 bases in length. The MM probes have a single base change in the center of the oligonucleotide sequence. Comparison of the hybridization signals from the PM and MM probes permits a measurement of the specificity of signal intensity, and eliminates from the data analysis the majority of non-specific cross hybridization. Values of intensity difference, as well as ratios of each probe pair, are used to determine whether a gene is “present”, i.e. the sample that was hybridized to the array expresses that genes transcript, or “absent”—there is no expression of that gene in the sample used for RNA extraction. To normalize between arrays (to remove experimental noise, such as differences in final cRNA quantity), each array was scaled using a target intensity of 100.  
      The resultant data was converted to Excel spreadsheets, and collated. As described above, each sample was processed in duplicate. Therefore all data analysis was performed on both the original expression values for each subject duplicate sample, plus the mean expression values of the duplicate subject samples. All gene expression values that were given an “absent call” were removed from the data sets. Gene expression data was filtered by removing all genes with expression levels less than two standard deviation above background levels. All statistical tests and data analysis were performed in Excel, except those described in detail below.  
      Data analysis; Hierarchical Clustering. Following normalization and filtering, unsupervised and supervised hierarchical clustering was performed using the Cluster program (M. Eisen, discussed Example A). The gene expression data was log-transformed and then median centered over each patient and control sample. Log intensity values for each gene (row), within each subject (column), were then normalized to set all the magnitudes (sum of the squares of the values) to 1.0. Average-linked clustering was performed on this adjusted dataset, employing a correlation centered metric. In this experiment, all genes and subjects were given an equal weighting of 1.0. The results of the clustering run were visualized using the program TreeView (M. Eisen).  
      Real-Time Polymerase Chain Reaction. 200 ng of total RNA from all patients and controls was employed for first strand cDNA synthesis, using random hexamer primers and Superscript II  Reverse Transcriptase enzyme (Invitrogen). Primers were designed using the Primer3 program (Whitehead Institute), except for the 18S ribosomal RNA primers, which were purchased as an internal standard PCR kit (Ambion). For real-time PCR the SYBR Green assay, which measures the linear binding of florescent molecules to double-stranded DNA at each cycle of the PCR amplification, was performed using the Quantitech Kit (Qiagen), on an ABI PRISM 7700 apparatus. The resultant florescence data was imported into Sequence Detector, v1.7a software (ABI), and Cts were calculated. The Ct (the PCR threshold cycle where an increase in reporter fluorescence above a baseline signal can first be detected) has a direct correlation with template concentration. The Cts of samples with known copy numbers were employed to generate standard amplification curves for each set of specific gene primers. Final copy numbers of each patient and control RNA sample were determined from each standard curve, and compared with the control 18S standard results.  
      Standard PCR protocols were also employed to analyze genes expressed at very low levels in subject leukocytes. cDNA was prepared as described above, and then employed as a template for PCR, using Hotstar polymerase enzyme (Qiagen) and a Hybaid PCR apparatus. Products were analyzed by staining with ethidium bromide following agarose gel electrophoresis. DNA was visualized using a gel documentation system (Kodak).  
     Results of the Preliminary Studies  
      Pair-wise Analysis of Microarray Results. To investigate total sample variability, a pair-wise comparison of expression levels was performed. It is expected that over 12,000 data points, samples should be highly correlated to allow meaningful comparison of the data. Correlation coefficients were within the range of 0.85-0.93 for each comparison (data not shown). In preliminary studies duplicate processing was performed, and pair-wise comparisons between duplicates showed high correlations between intra-subject samples. A scatter plot of expression data from patient A (sample A1-0 and A1-2) yielded an R 2  value of 0.967.  
      Analysis of gene expression from genes differentially regulated in peripheral blood. Expression level data for each of the genes previously found to be differentially regulated in peripheral blood were investigated. The mean expression levels were calculated across subjects processed to date from the two groups (mean expression values over duplicate samples). Decreased levels of MSH2 were observed (&gt;20% lower in patients than controls), which although is not significantly different between subject groups (p&gt;0.05), is consistent with the findings reported by Strom et al. (Strom et al., Prostate 2001; 47(4):269-75). Additionally, it was found that transcript levels of IFN gamma were decreased by &gt;20% in the patient leukocytes compared to control subjects. Decreasing levels of serum IFN gamma protein were previously found to correlate with increasing tumor mass (Elsasser-Beile et al., J Cancer Res Clin Oncol. 1993; 119(7):430-3), and the present data suggests that this correlation is directly related to decreased expression in patient peripheral blood leukocytes.  
      Of interest to this Example 4 in this invention, transcript levels of HER2 were found to be increased in the blood of prostate cancer patients when compared to control subjects (&gt;38% increased in patients versus control subjects). HER2, a proto-oncogenic member of the type 1 tyrosine kinase family is amplified in up to 30% of human breast cancers (Slamon et al., Science. 1987; 9; 235(4785):177-82), and serum levels of HER2, plus RT-PCR amplification of HER2 from circulating metastatic breast cancer cells are being explored as predictors of breast cancer patient survival (Willsher et al., Breast Cancer Res Treat. 1996; 40(3):251-5). Furthermore, many genes that were found to be altered to a much larger degree between the two subject groups than the genes described above, validating the experimental design of using a microarray approach to identify patterns of differentially regulated genes. Examples include the genes Megakaryocyte associated tyrosine kinase (116% decreased in patients versus controls, or &gt;3 fold decrease), programmed cell death-like cDNA (72% decreased in patients versus controls, or &gt;2.8 fold decrease) and MMP9 (40% increased in patients versus controls, or &gt;2 fold increase).  
      Analysis of IL-8 Leukocyte Gene expression. Veltri et al., supra, reported a significant increase in IL-8 gene expression in leukocytes from patients with metastatic disease, when compared to 18 transcript levels from a pool of control subjects. Analysis of expression levels following microarray hybridization of cRNA transcribed from each patient and control sample showed that IL-8 expression, although quite low, was not different between the two subject groups. The microarray IL-8 gene expression was investigated further, using a PCR based approach. cDNA was transcribed from each RNA sample, and then employed in a real-time PCR assay. To standardize input cDNA and thus RNA levels, PCR amplification products were normalized to the 18S ribosomal RNA gene. Thus real-time PCR was performed, employing 18S primers at concentrations that have been optimized to be in the range of amplification consistent with genes expressed at low levels (Ambion).  
      Real-Time PCR of the 18S Ribosomal RNA gene. The normalized SYBR Green signal (log Rn; Y axis) is plotted against PCR cycle number (X axis) for each sample. In this experiment, an arbitrary Ct was set to intersect each sample within the linear amplification stage of the PCR, and is represented by the dotted horizontal line. The samples show the control amplifications of a known sample concentration, at no dilution (1.0), 10 fold dilution, 100 fold and 1000 fold. Six subject sample 18S PCR amplifications are performed in duplicate.  
      A standard curve for 18S was generated, using dilutions of the control sample. The standard curve can be employed to determine both the relative concentration of starting template in each of the subject samples, as well as the actual numbers of molecules employed for analysis. The Cts calculated for each of the subject samples by the Sequence Detector, v1.7a software (ABI), were thus employed to determine the concentration of starting template for each of the samples which were found to be consistent with each other.  
      In the IL-8 assay, no DNA product was detected in any of the samples after 25 cycles of amplification (which is similar to PCR protocols followed by Veltri et al., Urology 1999; 53(1):139-47). After 40 PCR cycles, product was observed with a clear difference in IL-8 amplification was detected among the samples (data not shown). In each instance, levels of amplification were correlated with those detected following microarray hybridization described above. These results suggest that IL-8 expression is not a marker of localized prostate cancer, but increased expression levels of IL-8 may be a marker of metastatic disease, as detected by Veltri et al. (Veltri et al., supra).  
      Hierarchical Clustering of Prostate Cancer Patients and Control Subjects. Following normalization and filtering of the data, an unsupervised hierarchical clustering was initially performed, where data is analyzed in the Cluster program, with no previous set constraints on the data. For this analysis, the gene expression data was log transformed and then median centered over each patient and control sample. Following filtering of the data, an initial analysis of genes found to be called “present” in at least two of the samples processed to date was performed; thus a total of 6834 genes remained for further investigation. An unsupervised hierarchical clustering algorithm was implemented, employing the expression intensity levels of genes from 18 subjects. An average-linked cluster was performed on both absolute intensity values of each sample (n=18×2), and the mean intensity levels over the duplicate samples (n=18). Results from both Cluster analysis were viewed in the TreeView program (data not shown), and indicated that using the expression level measurements of 6834 genes, 90% of the prostate cancer patients clustered into one node. However, the classification was not exact as two control subjects also clustered into this node (data not shown).  
      Supervised Hierarchical Clustering Prostate Cancer Patients and Control Subjects. It may prove useful to perform a supervised clustering experiment, as surrogate tissue in which differences in the patterns of gene expression of leukocytes from tumor patients may be more subtle than the differences obtained from analysis of the tumor tissue itself. Other researchers investigating diagnostic gene expression profiles have performed supervised clustering by manipulating the data before input into the algorithm, for example Dhanasekaran et al. computed t-statistics of prostate cancer versus benign sample for each gene, to create a more limited and also more informative set of genes for analysis (Dhanasekaran et al., Nature. 2001; 412(6849):822-6). Following this example a student two-tailed t-test across the 6834 genes expressed in the patient and control subjects leukocytes was performed. Of the original 6834 genes, 896 were found to have expression values significantly different between the patients and controls (p&lt;0.05), and 1535 were found to have p&lt;0.1 between the two groups. Also performed was an identical student T-test on different permutations of randomized data, where subject samples were randomly placed into one of the two groups (using an approach similar to a permutation method for analysis of non-random data; Draghici et al., Drug Discov Today 2002; 7(11):S55-S63). It was found that the average number of genes found to be significantly different between the randomized groups was 200 (p&lt;0.05), while &lt;500 genes were found to have p&lt;0.1. A t-test performed on the p-values of the “real” group versus the random groups showed a significant difference between groups (p&lt;0.0001). Therefore, randomizing the data results in nearly 80% less genes found to be significantly different between subject groups and may represent the noise of this experimental system.  
      TreeView Representation of Cluster patterns of gene expression among men with prostate cancer and age-matched control subjects ( FIG. 1 ). Data are represented in matrix format. Each row represents a single gene (for space gene names have been omitted). Each column represents an experimental leukocyte patient or control sample. For each sample the ratio of the abundance of transcripts of each gene, to the median abundance of the genes&#39;s transcript among the individuals leukocytes, is represented by the color of the corresponding matrix. Green means that transcript levels are less than median; black means the transcript levels are median; red means the transcript levels are greater than median. Grey is used to indicate that the gene is absent. Color saturation represents the magnitude of the ratio relative to the median for the total set of samples. A dendrogram along the horizontal axis indicates the clusters of most similar subjects, based on gene expression levels of 1535 genes. The dendrogram along the vertical axis represents sample nodes of the total Cluster results, where genes appear together on the branches of the tree if they have similar patterns of gene expression. Examples of Cluster nodes are taken from the total TreeView data, showing genes that are generally expressed at lower levels in the prostate cancer samples (A1 to A13), than control subject samples (B1 to B7). A scaled representation of the horizontal dendrogram showing patient and control cluster results can be shown.  
      The 1535 genes (p&lt;0.1) were further analyzed employing the Cluster program with readout in TreeView. Again, this analysis was performed using both the mean of duplicate subject samples and the absolute intensity levels of each sample.  FIG. 1  shows an example of this data analysis, where mean intensity levels were employed for all but three samples. The results of this supervised cluster analysis indicates that the overall leukocyte expression of 1535 genes from the 11 prostate cancer patients is different to the overall gene expression data of the seven control subjects. Specifically, the prostate cancer patients cluster in a node that is separate to the node of control subjects, and suggests that distinctive patterns of gene expression can be employed to differentiate between prostate cancer patients and control subjects. The use of duplicate samples permits a finding that experimental difference (as observed between B2-0 and B2-1), do not influence the final cluster results.  
      To perform an investigation on this clustering result, subject gene expression levels were randomized within the dataset and the resultant data were re-clustered. Five different re-iterations of randomizing the data were performed. A TreeView readout from the clustering of 1535 genes, where subjects have been classified into one of two nodes representing cancer patients or control subjects, and a TreeView readout generated following Cluster analysis of the randomized dataset was used to analyze the data ( FIG. 2 ). Short branch lengths between each node of the dendrogram of random data show that following intra-subject randomization, patient samples have overall gene expression patterns very similar to each other. Furthermore, the dendrogram has not organized the samples into an order significantly different from the initial order of data input into the Cluster algorithm and duplicate samples are dispersed over the tree. The Cluster analysis of the other random data iterations resulted in TreeView readouts where either the samples remained in the order of input into Cluster, or alternatively branch lengths were observed to be vastly reduced, indicating very minor differences in overall gene expression between subjects. These results suggest that this supervised hierarchical clustering, which demonstrates a correct classification of prostate cancer patients and control subjects into their respective groups, is not due to random microarray data.  
      Table 1 shows a list of genes from PBLs up- or down-regulated in prostate cancer subjects.  
               TABLE 1                          Prostate Cancer Gene Expression Results       This table includes gene expression profile data from 11 prostate cancer patients       versus 6 control subjects. The table includes the Affymetrix probe-set ID for the HU95Av2       GeneChip array, and also the EASE assignment. The EASE data were included because       there are instances where an unknown EST (as referenced to by the Affymetrix probeset       ID) has later been characterized by others. However, these curation methods are not 100%       accurate.       It is very important to note that the significance levels for the genes/ESTs can       change with increasing statistical power from comparing additional samples. Therefore, it       may be likely that some genes/ESTs may change in significance.                                 Mean levels                   expression in   two tailed       Affymetrix   prostate cancer   Students       HU95A version2   patients compared   t-test   EASE Names       probe set ids   to healthy controls   significance   (david.niaid.nih.gov/david/ease.h               37046_at   down   1.95E−07   proteasome (prosome, macropain) subunit, alpha type, 5       2010_at   down    3.1E−07   S-phase kinase-associated protein 1A (p19A)       36546_r_at   up   1.66E−06   KIAA0542 gene product       33602_at   up   4.77E−06   endothelial differentiation, G-protein-coupled receptor 6       36591_at   up    4.9E−06   tubulin, alpha 1 (testis specific)       33190_g_at   up   5.31E−06   chromosome 10 open reading frame 6       32595_at   down    6.5E−06   G-rich RNA sequence binding factor 1       39030_at   up   7.14E−06   Rab acceptor 1 (prenylated)       36567_at   up   7.59E−06   solute carrier family 17 (sodium-dependent inorganic                   phosphate cotransporter), member 7       32066_g_at   up   9.85E−06   cAMP responsive element modulator       38964_r_at   up   1.15E−05   Wiskott-Aldrich syndrome (eczema-thrombocytopenia)       35485_at   up   1.35E−05   glutamate receptor, metabotropic 4       32622_at   up   1.53E−05   dynamin 2       33126_at   down    1.7E−05   glycosyltransferase AD-017       38621_at   up    1.9E−05   dimethylarginine dimethylaminohydrolase 2       31620_at   up   2.07E−05   similar to transcription factor TBX10       330_s_at   up   2.28E−05   Tubulin, Alpha 1, isoform 44       32378_at   up   2.76E−05   pyruvate kinase, muscle       36098_at   down   2.87E−05   splicing factor, arginine/serine-rich 1 (splicing factor 2,                   alternate splicing factor)       1268_at   up   3.43E−05   ubiquitin-activating enzyme E1 (A1S9T and BN75                   temperature sensitivity complementing)       31391_at   up   6.24E−05   huntingtin-associated protein 1 (neuroan 1)       39797_at   down   6.39E−05   ubiquitin ligase E3 alpha-II       1660_at   down    6.4E−05   ubiquitin-conjugating enzyme E2N (UBC13 homolog,                   yeast)       31901_at   up    7.3E−05   potassium voltage-gated channel, shaker-related                   subfamily, beta member 2       1772_s_at   down   7.48E−05   farnesyltransferase, CAAX box, alpha       36994_at   up   8.05E−05   ATPase, H+ transporting, lysosomal 16 kDa, V0 subunit c       32659_at   down   8.47E−05   eukaryotic translation initiation factor 2B, subunit 4 delta,                   67 kDa       41248_at   down   9.53E−05   likely ortholog of mouse variant polyadenylation protein                   CSTF-64       39709_at   up   0.000116   selenoprotein W, 1       31740_s_at   up   0.000125   paired box gene 4       40418_at   down   0.000125   retinoblastoma binding protein 4       39792_at   down   0.000141   heterogeneous nuclear ribonucleoprotein R       41078_at   up   0.000149   KIAA0150 protein       31341_at   up   0.000154   potassium voltage-gated channel, Shaw-related                   subfamily, member 3       32163_f_at   up   0.000157   chorionic somatomammotropin hormone 2       676_g_at   up   0.000162   interferon induced transmembrane protein 1 (9-27)       34832_s_at   up   0.000163   KIAA0763 gene product       924_s_at   down   0.000166   protein phosphatase 2 (formerly 2A), catalytic subunit,                   beta isoform       34491_at   up   0.000166   2′-5′-oligoadenylate synthetase-like       1392_at   up   0.000172   G protein-coupled receptor kinase 6       39118_at   down   0.000176   DnaJ (Hsp40) homolog, subfamily A, member 1       34141_at   up   0.000188       31785_f_at   up   0.000197   unnamed HERV-H protein       41219_at   down   0.000227   KIAA0570 gene product       38105_at   down   0.000234   hypothetical protein FLJ11021 similar to splicing factor,                   arginine/serine-rich 4       37334_at   down   0.000239   heterogeneous nuclear ribonucleoprotein A0       40452_at   up   0.000249   copine I       32784_at   down   0.000259   PRP4 pre-mRNA processing factor 4 homolog B (yeast)       31968_at   up   0.000266       36907_at   up   0.000271   mevalonate kinase (mevalonic aciduria)       35577_at   up   0.000275   serine (or cysteine) proteinase inhibitor, clade B                   (ovalbumin), member 7       32115_r_at   up   0.000285   adenosine A2a receptor       1577_at   up   0.000288   androgen receptor (dihydrotestosterone receptor;                   testicular feminization; spinal and bulbar muscular                   atrophy; Kennedy disease)       1830_s_at   up   0.000295   transforming growth factor, beta 1 (Camurati-Engelmann                   disease)       33803_at   down   0.000306   thrombomodulin       41159_at   down   0.000311   clathrin, heavy polypeptide (Hc)       1158_s_at   up   0.000315   calmodulin 3 (phosphorylase kinase, delta)       39162_at   down   0.000328   Arg/Abl-interacting protein ArgBP2       37201_at   up   0.000335   inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-                   sensitive glycoprotein)       37383_f_at   up   0.000338   major histocompatibility complex, class I, C       41836_at   down   0.000345   calcium homeostasis endoplasmic reticulum protein       38963_i_at   up   0.000349   Wiskott-Aldrich syndrome (eczema-thrombocytopenia)       34827_at   up   0.000362   unc-51-like kinase 1 ( C. elegans )       37074_at   up   0.00037   syntrophin, beta 1 (dystrophin-associated protein A1,                   59 kDa, basic component 1)       37746_r_at   up   0.000372   suppression of tumorigenicity 5       37267_at   up   0.000373   thimet oligopeptidase 1       33779_at   up   0.000386   vesicle-associated membrane protein 1 (synaptobrevin 1)       457_s_at   down   0.000395   ubiquitin-like 1 (sentrin)       41745_at   up   0.000404   interferon induced transmembrane protein 3 (1-8U)       37468_at   down   0.000419   Janus kinase 2 (a protein tyrosine kinase)       35802_at   down   0.000424   formin binding protein 4       1698_at   down   0.000429   polymerase (DNA directed), beta       38409_at   down   0.000433   sperm specific antigen 2       38093_at   down   0.000442   chromosome 14 open reading frame 32       36143_at   down   0.000469   caspase 3, apoptosis-related cysteine protease       34151_at   up   0.000471   DKFZP586M1019 protein       41033_at   down   0.000475   zinc finger protein 84 (HPF2)       32053_at   down   0.000477   cyclin T2       38865_at   up   0.000509   GRB2-related adaptor protein 2       36377_at   up   0.00052   interleukin 18 receptor 1       37977_at   up   0.00052   deltex homolog 2 ( Drosophila )       32447_at   up   0.000538   nuclear receptor subfamily 5, group A, member 1       36926_at   down   0.00055   mitogen-activated protein kinase 6       869_at   down   0.000554   general transcription factor IIA, 2, 12 kDa       34604_at   up   0.000585   solute carrier family 6 (neurotransmitter transporter,                   serotonin), member 4       41795_at   down   0.000605   NCK adaptor protein 1       33542_at   up   0.00061       40355_at   up   0.000621   AND-1 protein       40585_at   down   0.000638   adenylate cyclase 7       34384_at   down   0.000654   ATP-binding cassette, sub-family C (CFTR/MRP),                   member 1       34907_at   up   0.000654   apoptosis-associated tyrosine kinase       2058_s_at   up   0.000655   integrin, beta 5       35899_at   up   0.000659   artemin       140_s_at   down   0.000663   splicing factor, arginine/serine-rich 10 (transformer 2.                   homolog,  Drosophila )       40976_at   up   0.000674   katanin p80 (WD repeat containing) subunit B 1       33180_at   down   0.000681   protein phosphatase 1, regulatory (inhibitor) subunit 2       34157_f_at   up   0.000685   histone 1, H2al       32080_at   up   0.000692   tetracycline transporter-like protein       39336_at   up   0.000697   ADP-ribosylation factor 3       36675_r_at   up   0.000703   profilin 1       36720_at   up   0.000705   pyruvate dehydrogenase kinase, isoenzyme 3       38223_at   down   0.000723   TBC1 domain family, member 8 (with GRAM domain)       32198_at   up   0.000738   hypothetical protein FLJ20452       40007_at   up   0.000744   zinc finger protein, subfamily 1A, 1 (Ikaros)       1351_at   up   0.000757   EphB4       1307_at   down   0.000757   xeroderma pigmentosum, complementation group A       36258_at   up   0.000769   protein kinase, cGMP-dependent, type I       37692_at   down   0.000799   diazepam binding inhibitor (GABA receptor modulator,                   acyl-Coenzyme A binding protein)       32548_at   down   0.000801   unactive progesterone receptor, 23 kD       38608_at   up   0.000802   lectin, galactoside-binding, soluble, 7 (galectin 7)       37968_at   up   0.000806   natural cytotoxicity triggering receptor 3       39091_at   down   0.000806   vitamin A responsive; cytoskeleton related       39057_at   up   0.000808   kinesin 2 60/70 kDa       33226_at   up   0.00082   KIAA0876 protein       40580_r_at   up   0.000825   parathymosin       41428_at   up   0.000843   ATP-binding cassette, sub-family C (CFTR/MRP),                   member 5       354_s_at   down   0.000847   RecQ protein-like (DNA helicase Q1-like)       34694_at   up   0.000848   SWI/SNF related, matrix associated, actin dependent                   regulator of chromatin, subfamily d, member 2       32433_at   down   0.00085       34098_f_at   up   0.000893   integrin cytoplasmic domain-associated protein 1       34062_at   up   0.000902   ets variant gene 2       38967_at   down   0.000913   chromosome 14 open reading frame 2       34330_at   down   0.000915   cytochrome c oxidase subunit VIIa polypeptide 2 like       32201_at   up   0.000925   Sjogren&#39;s syndrome nuclear autoantigen 1       1127_at   up   0.000936   ribosomal protein S6 kinase, 90 kDa, polypeptide 1       40268_at   up   0.000942   FOS-like antigen 2       36023_at   down   0.000951   proline-rich protein HaeIII subfamily 1       AFFX-CreX-3_st   up   0.000965       33913_at   up   0.000995   HLA-B associated transcript 2       37838_at   up   0.001007   coagulation factor XII (Hageman factor)       37098_at   up   0.001029   protoporphyrinogen oxidase       1333_f_at   up   0.001043   breakpoint cluster region       32904_at   up   0.001057   perforin 1 (pore forming protein)       33103_s_at   down   0.001068   adducin 3 (gamma)       34811_at   down   0.001072   ATP synthase, H+ transporting, mitochondrial F0 complex,                   subunit c (subunit 9) isoform 3       40504_at   up   0.001073   paraoxonase 2       33764_at   up   0.001075   G protein-coupled receptor 51       35626_at   up   0.001085   N-sulfoglucosamine sulfohydrolase (sulfamidase)       38726_at   up   0.001085   dolichyl-phosphate mannosyltransferase polypeptide 2,                   regulatory subunit       1794_at   up   0.001089   cyclin D3       534_s_at   up   0.001117   folate receptor 1 (adult)       34714_at   down   0.001123   SAM domain and HD domain 1       1452_at   down   0.001145   LIM domain only 4       35132_at   up   0.001152   myosin IF       40947_at   up   0.001185   hypothetical protein FLJ12671       36343_at   up   0.001189   tolloid-like 2       35693_at   up   0.001227   hippocalcin-like 1       34486_at   up   0.001262       34702_f_at   up   0.001285   chorionic somatomammotropin hormone 2       35171_at   down   0.00129   spastic paraplegia 4 (autosomal dominant; spastin)       38057_at   up   0.001298   dermatopontin       41333_at   down   0.001302   centaurin, beta 2       34703_f_at   up   0.001305   chorionic somatomammotropin hormone 2       41821_at   down   0.001307   cell division cycle 2-like 5 (cholinesterase-related cell                   division controller)       41788_i_at   down   0.001308   KIAA0669 gene product       37604_at   down   0.001315   histamine N-methyltransferase       921_s_at   up   0.001335       39444_at   down   0.001337   splicing factor 3b, subunit 1, 155 kDa       38072_at   down   0.001339   hypothetical protein dJ465N24.2.1       39624_at   up   0.001377   leukotriene B4 receptor       AFFX-   up   0.001382   actin, beta       HSAC07/X00351_M_at       38449_at   up   0.0014   WD repeat domain 23       39353_at   down   0.001411   heat shock 10 kDa protein 1 (chaperonin 10)       40260_g_at   up   0.001416   RNA binding motif protein 9       33372_at   up   0.001431   RAB31, member RAS oncogene family       39166_s_at   up   0.001476   serine (or cysteine) proteinase inhibitor, clade H (heat                   shock protein 47), member 1, (collagen binding protein 1       40138_at   up   0.00148   COP9 subunit 6 (MOV34 homolog, 34 kD)       35451_s_at   up   0.001495   SCAN domain containing 2       34802_at   up   0.001519   collagen, type VI, alpha 2       36654_s_at   down   0.00153   heterogeneous nuclear ribonucleoprotein A2/B1       33887_at   up   0.00159   hepatocyte growth factor-regulated tyrosine kinase                   substrate       39748_at   down   0.001591       35753_at   up   0.001648   PRP8 pre-mRNA processing factor 8 homolog (yeast)       41752_at   down   0.001662   growth hormone inducible transmembrane protein       31926_at   up   0.001667   cytochrome P450, family 7, subfamily A, polypeptide 1       32407_f_at   up   0.001671       39909_g_at   up   0.001683   TAF6-like RNA polymerase II, p300/CBP-associated                   factor (PCAF)-associated factor, 65 kDa       36270_at   down   0.001685   CD86 antigen (CD28 antigen ligand 2, B7-2 antigen)       40359_at   up   0.001688   chromosome 11 open reading frame 13       39079_at   down   0.001696   enhancer of rudimentary homolog ( Drosophila )       650_s_at   down   0.001755   calcium/calmodulin-dependent protein kinase (CaM                   kinase) II gamma       33783_at   up   0.001762   plexin B1       39119_s_at   up   0.001784   natural killer cell transcript 4       36814_at   down   0.001798   hypothetical protein KIAA1109       40518_at   down   0.001806   protein tyrosine phosphatase, receptor type, C       34056_g_at   up   0.001806   activin A receptor, type IB       40110_at   down   0.001822   isocitrate dehydrogenase 3 (NAD+) beta       421_at   up   0.001832   translocated promoter region (to activated MET                   oncogene)       37386_i_at   up   0.001833   KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein                   retention receptor 1       32803_at   down   0.001853   comichon homolog ( Drosophila )       38336_at   up   0.001856   GRP1-binding protein GRSP1       34263_s_at   down   0.001864   diaphanous homolog 2 ( Drosophila )       39949_at   up   0.001866   molybdenum cofactor synthesis 1       36715_at   up   0.001899   adrenergic, alpha-1A-, receptor       38500_at   down   0.001906   CGI-109 protein       31557_at   up   0.001915   thymosin, beta 4, X chromosome       32206_at   up   0.001916   CDC42 binding protein kinase alpha (DMPK-like)       34819_at   down   0.001946   CD164 antigen, sialomucin       40988_at   down   0.001949   YME1-like 1 ( S. cerevisiae )       38982_at   down   0.001952   telomeric repeat binding factor 2, interacting protein       31610_at   up   0.001954   membrane-associated protein 17       33378_at   down   0.001956   IDN3 protein       34353_at   down   0.00196   KIAA0648 protein       41529_g_at   down   0.001972       36895_at   down   0.001975   origin recognition complex, subunit 3-like (yeast)       38814_at   down   0.001995   ATPase, H+ transporting, lysosomal 13 kDa, V1 subunit                   isoform 1       35986_at   up   0.001998   MYST histone acetyltransferase 1       37075_at   up   0.002003   syntrophin, beta 1 (dystrophin-associated protein A1,                   59 kDa, basic component 1)       37358_at   down   0.002024   ubiquitin-conjugating enzyme E2E 1 (UBC4/5 homolog,                   yeast)       37995_s_at   down   0.002036   fragile X mental retardation 1       36694_at   up   0.00204   potassium voltage-gated channel, delayed-rectifier,                   subfamily S, member 3       35804_at   down   0.002047   ash2 (absent, small, or homeotic)-like ( Drosophila )       34409_at   up   0.002066   low density lipoprotein receptor-related protein 10       40360_at   up   0.002068   Protein P3       35600_at   down   0.00209   ROD1 regulator of differentiation 1 ( S. pombe )       32005_at   up   0.002111   pro-melanin-concentrating hormone       40489_at   up   0.002142   dentatorubral-pallidoluysian atrophy (atrophin-1)       38355_at   down   0.002155   DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide, Y                   chromosome       41598_at   down   0.002175   SEC22 vesicle trafficking protein-like 1 ( S. cerevisiae )       193_at   down   0.002179   TAF9 RNA polymerase II, TATA box binding protein                   (TBP)-associated factor, 32 kDa       41756_at   down   0.002228   XPA binding protein 1       40509_at   down   0.00226   electron-transfer-flavoprotein, alpha polypeptide (glutaric                   aciduria II)       36981_at   down   0.002271   signal recognition particle 9 kDa       400 _at   down   0.002273   mago-nashi homolog, proliferation-associated                   ( Drosophila )       40698_at   down   0.002275   C-type (calcium dependent, carbohydrate-recognition                   domain) lectin, superfamily member 2 (activation-induced       33664_g_at   up   0.002278       37389_at   down   0.002286   small acidic protein       640_at   up   0.002306   angiotensin II receptor-like 2       37031_at   down   0.002324   chromosome 9 open reading frame 10       40844_at   down   0.00233   SH2 domain binding protein 1 (tetratricopeptide repeat                   containing)       35735_at   down   0.002374   guanylate binding protein 1, interferon-inducible, 67 kDa       254_at   down   0.002379   H3 histone, family 3A       32232_at   down   0.002401   NADH dehydrogenase (ubiquinone) 1 beta subcomplex,                   5, 16 kDa       39039_s_at   down   0.002472   ubiquitin-conjugating enzyme E2, J1 (UBC6 homolog,                   yeast)       35768_at   up   0.002473   ring finger protein 40       37145_at   up   0.002506   granulysin       41360_at   down   0.002506   CCR4-NOT transcription complex, subunit 8       1798_at   down   0.002559   LIV-1 protein, estrogen regulated       322_at   up   0.002593   phosphoinositide-3-kinase, regulatory subunit, polypeptide                   3 (p55, gamma)       35035_at   up   0.002603   cholinergic receptor, nicotinic, beta polypeptide 3       34558_at   up   0.002611   opiate receptor-like 1       32789_at   down   0.002639   nuclear cap binding protein subunit 2, 20 kDa       32422_at   up   0.002657   double C2-like domains, beta       31388_at   up   0.002677   early lymphoid activation protein       38880_at   up   0.002701   likely ortholog of mouse mitogen activated protein kinase                   binding proten 1       34611_at   up   0.002705   zinc finger protein 192       39629_at   up   0.002729   phospholipase A2, group V       1827_s_at   up   0.002732   v-myc myelocytomatosis viral oncogene homolog (avian)       34786_at   down   0.002751   jumonji domain containing 1       652_g_at   down   0.002754   replication protein A3, 14 kDa       38480_s_at   up   0.002774   ubiquitin-conjugating enzyme E2I (UBC9 homolog, yeast)       38860_at   up   0.002779   phosphodiesterase 4C, cAMP-specific                   (phosphodiesterase E1 dunce homolog,  Drosophila )       39083_at   down   0.002817   ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog,                   yeast)       38589_l_at   down   0.00284   prothymosin, alpha (gene sequence 28)       38753_at   down   0.002847   exportin, tRNA (nuclear export receptor for tRNAs)       41423_at   up   0.002861   calsyntenin 3       36474_at   down   0.002868   KIAA0776 protein       34336_at   down   0.00288   lysyl-tRNA synthetase       184_at   up   0.002913   angiotensin II receptor-like 1       33546_at   up   0.002927       40044_at   up   0.002937   ELL gene (11-19 lysine-rich leukemia gene)       2031_s_at   up   0.002964   cyclin-dependent kinase inhibitor 1A (p21, Cip1)       34178_at   up   0.002967   zinc finger protein 297       33098_at   down   0.003008   chemokine (C—C motif) receptor 3       955_at   up   0.003035   Calmodulin Type 1       33440_at   down   0.00306   transcription factor 8 (represses interleukin 2 expression       31870_at   up   0.003092   CD37 antigen       31861_at   up   0.003094   immunoglobulin mu binding protein 2       36949_at   up   0.00313   casein kinase 1, delta       35681_r_at   down   0.003133   zinc finger homeobox 1b       1848_at   down   0.003145   RAP1A, member of RAS oncogene family       41612_at   up   0.003146   zinc finger protein 264       40038_at   up   0.003148   suppression of tumorigenicity 7       35749_at   up   0.003152   transcriptional adaptor 3 (NGG1 homolog, yeast)-like       38370_at   down   0.00316       33848_r_at   down   0.003175   cyclin-dependent kinase inhibitor 1B (p27, Kip1)       35426_at   up   0.003201   SPPL2b       33417_at   up   0.003215   RAB3 GTPase-ACTIVATING PROTEIN       36791_g_at   up   0.003221   tropomyosin 1 (alpha)       38822_at   up   0.003235   serine/threonine kinase 17a (apoptosis-inducing)       40481_r_at   up   0.003244   FYN oncogene related to SRC, FGR, YES       36805_s_at   up   0.003265   neurotrophic tyrosine kinase, receptor, type 1       31519_f_at   down   0.003267   basic transcription factor 3, like 3       37844_at   down   0.003277   class I cytokine receptor       39553_at   down   0.003292   phosphatase and tensin homolog (mutated in multiple                   advanced cancers 1)       41386_i_at   up   0.003297   KIAA0346 protein       41141_at   down   0.003301   protein-kinase, interferon-inducible double stranded RN                   dependent inhibitor, repressor of (P58 repressor)       40957_at   down   0.003302   joined to JAZF1       33820_g_at   down   0.00335   lactate dehydrogenase B       36688_at   down   0.003368   sterol carrier protein 2       1760_s_at   up   0.003403   protein tyrosine phosphatase, non-receptor type 7       31584_at   down   0.003438   tumor protein, translationally-controlled 1       40610_at   down   0.003441   zinc finger RNA binding protein       108_g_at   up   0.003453       32590_at   down   0.003459   nucleolin       38516_at   up   0.003465   sodium channel, voltage-gated, type I, beta       33113_at   down   0.003483   Cbp/p300-interacting transactivator, with Glu/Asp-rich                   carboxy-terminal domain, 2       34337_s_at   down   0.003512   likely ortholog of mouse metal response element binding                   transcription factor 2       35976_at   up   0.003514   Cbp/p300-interacting transactivator, with Glu/Asp-rich                   carboxy-terminal domain, 1       33622_at   up   0.003533   calcium channel, voltage-dependent, L type, alpha 1C                   subunit       552_at   up   0.003551   Rho GTPase activating protein 1       36571_at   down   0.00356   topoisomerase (DNA) II beta 180 kDa       36887_f_at   up   0.003595   killer cell immunoglobulin-like receptor, three domains,                   long cytoplasmic tail, 1       1662_r_at   up   0.003647   Antigen, Prostate Specific, Alt. Splice Form 2       40555_at   down   0.003673   ras homolog gene family, member Q       1389_at   up   0.003688   membrane metallo-endopeptidase (neutral                   endopeptidase, enkephalinase, CALLA, CD10)       37729_at   down   0.003702   exportin 1 (CRM1 homolog, yeast)       34485_r_at   up   0.003769   ADP-ribosylation factor guanine nucleotide-exchange                   factor 2 (brefeldin A-inhibited)       582_g_at   down   0.003786   nuclear receptor subfamily 2, group C, member 1       38415_at   down   0.003786   protein tyrosine phosphatase type IVA, member 2       2070_i_at   up   0.003801   mitogen-activated protein kinase 8       40392_at   up   0.003801   caudal type homeo box transcription factor 2       35761_at   down   0.003805   aminoadipate-semialdehyde dehydrogenase-                   phosphopantetheinyl transferase       36793_at   up   0.003865   hypothetical protein AY099107       31859_at   up   0.003871   matrix metalloproteinase 9 (gelatinase B, 92 kDa                   gelatinase, 92 kDa type IV collagenase)       40928_at   down   0.003876   SOCS box-containing WD protein SWiP-1       41253_s_at   down   0.003901   chorionic somatomammotropin hormone 2       1724_at   up   0.003958   E2F transcription factor 4, p107/p130-binding       37448_s_at   up   0.003965   GNAS complex locus       34081_at   up   0.004003       40098_at   up   0.004012   EH-domain containing 1       38915_at   up   0.004044   KIAA0563 gene product       37523_at   up   0.004046   acyl-Coenzyme A dehydrogenase, long chain       36179_at   up   0.004048   mitogen-activated protein kinase-activated protein kinase 2       37481_at   down   0.00405   cell division cycle 40 homolog (yeast)       40376_at   up   0.004057   arylsulfatase E (chondrodysplasia punctata 1)       1862_at   up   0.004074   ataxia telangiectasia mutated (includes complementation                   groups A, C and D)       40497_at   up   0.004088   homologous to yeast nitrogen permease (candidate tumor                   suppressor)       35317_at   down   0.004109   meningioma expressed antigen 5 (hyaluronidase)       2051_at   up   0.004115   O-6-methylguanine-DNA methyltransferase       1759_f_at   up   0.00415   cytochrome P450, family 3, subfamily A, polypeptide 7       35842_at   down   0.00418       276_at   down   0.004191   DnaJ (Hsp40) homolog, subfamily A, member 1       38661_at   up   0.004217   RNA-binding region (RNP1, RRM) containing 1       39086_g_at   down   0.004239   single-stranded DNA binding protein       35861_at   up   0.004246   sialyltransferase 4A (beta-galactoside alpha-2,3-                   sialyltransferase)       38756_at   up   0.004248   RAP1A, member of RAS oncogene family       34441_at   up   0.004253       AFFX-   up   0.004262   actin, beta       HSAC07/X00351_5_at       39169_at   down   0.004272   Sec61 gamma       1128_s_at   up   0.004279   chemokine (C—C motif) receptor 1       38882_r_at   up   0.004292   tripartite motif-containing 16       1929_at   down   0.004324   angiopoietin 1       32088_at   down   0.004339   basic leucine zipper nuclear factor 1 (JEM-1)       38558_at   up   0.004345   myelin associated glycoprotein       31385_at   up   0.004347   ribosomal protein L28       32011_g_at   up   0.004354   hypothetical protein EAN57       494_at   up   0.004374   interleukin 13       38326_at   up   0.004396   putative lymphocyte G0/G1 switch gene       33351_at   down   0.004415   translation factor sui1 homolog       34885_at   up   0.004455   synaptogyrin 2       38443_at   down   0.004483   protein tyrosine phosphatase, non-receptor type 11                   (Noonan syndrome 1)       40643_at   up   0.004486   integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa                   complex, antigen CD41B)       37769_at   up   0.004498   endothelial differentiation, lysophosphatidic acid G-                   protein-coupled receptor, 4       34307_at   down   0.004507   transmembrane 9 superfamily member 2       40083_at   down   0.004509   KIAA0625 protein       40649_at   up   0.004524   proprotein convertase subtilisin/kexin type 1       32227_at   down   0.004544   proteoglycan 1, secretory granule       36114_r_at   up   0.004572   troponin T1, skeletal, slow       31549_at   up   0.004598   MAS1 oncogene       39688_at   up   0.004617   requiem, apoptosis response zinc finger gene       1620_at   up   0.004646   cadherin 6, type 2, K-cadherin (fetal kidney)       40601_at   down   0.004663   beta-amyloid binding protein precursor       AFFX-BioDn-   up   0.004695       5_st       39145_at   up   0.004699   myosin, light polypeptide 9, regulatory       1091_at   up   0.004758   protein kinase, cAMP-dependent, regulatory, type I, beta       36029_at   up   0.004763   chromosome 11 open reading frame 8       41237_at   up   0.004771   major histocompatibility complex, class I, A       1104_s_at   up   0.004778   heat shock 70 kDa protein 1A       38590_r_at   down   0.004787   prothymosin, alpha (gene sequence 28)       38280_s_at   up   0.004802   neurotrophic tyrosine kinase, receptor, type 2       40943_at   up   0.004812   ELOVL family member 6, elongation of long chain fatty                   acids (FEN1/Elo2, SUR4/Elo3-like, yeast)       36557_at   up   0.004814   calcium channel, voltage-dependent, beta 1 subunit       759_at   up   0.004832   prostaglandin I2 (prostacyclin) synthase       201_s_at   up   0.004856   beta-2-microglobulin       36581_at   down   0.004873   glycyl-tRNA synthetase       39825_at   up   0.00488   solute carrier family 25 (mitochondrial carrier; citrate                   transporter), member 1       31471_at   up   0.004912       37511_at   up   0.004922   B9 protein       33948_at   up   0.004978   corticotropin releasing hormone receptor 2       39594_f_at   up   0.005046   metallothionein 1H       41154_r_at   down   0.005048   catenin (cadherin-associated protein), alpha 1, 102 kDa       36173_r_at   down   0.005061   adaptor-related protein complex 3, delta 1 subunit       41812_s_at   down   0.005062   nucleoporin 210       34879_at   down   0.005073   dolichyl-phosphate mannosyltransferase polypeptide 1,                   catalytic subunit       33301_g_at   up   0.005075   cell division cycle 2-like 2       32701_at   up   0.005095   armadillo repeat gene deletes in velocardiofacial                   syndrome       37450_r_at   up   0.005122   GNAS complex locus       600_at   down   0.005135   RAB5A, member RAS oncogene family       1064_at   down   0.005246   PTK9 protein tyrosine kinase 9       38562_g_at   up   0.005247   down-regulated in metastasis       41850_s_at   up   0.005324   hepatitis delta antigen-interacting protein A       35826_at   up   0.005331   suppressor of Ty 5 homolog ( S. cerevisiae )       38820_at   down   0.005384   15 kDa selenoprotein       1269_at   down   0.005394   phosphoinositide-3-kinase, regulatory subunit, polypeptic                   1 (p85 alpha)       37726_at   down   0.005424   mitochondrial ribosomal protein L3       34155_s_at   up   0.005435   tyrosinase (oculocutaneous albinism IA)       37296_at   down   0.005438   ADP-ribosylation factor-like 1       38060_at   down   0.005484   NADH dehydrogenase (ubiquinone) Fe—S protein 5,                   15 kDa (NADH-coenzyme Q reductase)       36734_at   up   0.005503   small proline-rich protein 2A       36107_at   down   0.005549   ATP synthase, H+ transporting, mitochondrial F0 comple                   subunit F6       36961_at   down   0.00558   cervical cancer 1 protooncogene       31386_at   up   0.005585   immunoglobulin kappa variable 1/OR15-118       38939_r_at   up   0.00562   T-box, brain, 1       34824_at   down   0.005649   ubiquilin 2       41443_at   up   0.005702   SEC7 homolog       411_i_at   up   0.005711   interferon induced transmembrane protein 2 (1-8D)       32442_at   up   0.005715       31481_s_at   down   0.005719   thymosin, beta 10       32726_g_at   down   0.005746   BH3 interacting domain death agonist       34326_at   down   0.005796   coatomer protein complex, subunit beta       126_s_at   up   0.005887   synovial sarcoma, X breakpoint 2       40027_at   down   0.005902   ATP synthase, H+ transporting, mitochondrial F0 comple                   subunit s (factor B)       324_f_at   down   0.005902       41292_at   down   0.005909   heterogeneous nuclear ribonucleoprotein H1 (H)       32394_s_at   down   0.005972   ribosomal protein L23       37560_at   up   0.006036   FLJ00133 protein       38398_at   up   0.006052   MAP-kinase activating death domain       38448_at   up   0.006057   actinin, alpha 2       32859_at   down   0.006069   signal transducer and activator of transcription 1, 91 kDa       33535_at   up   0.006079   purinergic receptor P2X, ligand-gated ion channel, 1       35886_at   up   0.006119   protein kinase C and casein kinase substrate in neurons       1930_at   up   0.00618   ATP-binding cassette, sub-family C (CFTR/MRP),                   member 3       37970_at   up   0.006192   mitogen-activated protein kinase 8 interacting protein 3       41677_at   down   0.006198   interleukin 15 receptor, alpha       38966_at   up   0.006205   glycoprotein, synaptic 2       40137_at   down   0.006261   protein tyrosine phosphatase, non-receptor type 1       32010_at   up   0.006291   hypothetical protein EAN57       34557_at   up   0.006316   melanocortin 1 receptor (alpha melanocyte stimulating                   hormone receptor)       39310_at   up   0.006345   bradykinin receptor B2       38412_at   up   0.006424   protein phosphatase 1, regulatory (inhibitor) subunit 11       35266_at   down   0.006494   bladder cancer associated protein       37693_at   down   0.006535   numb homolog ( Drosophila )       32802_at   down   0.00654   similar to  S. cerevisiae  SSM4       39099_at   down   0.00654   Sec23 homolog A ( S. cerevisiae )       41376_i_at   up   0.006549   UDP glycosyltransferase 2 family, polypeptide B7       38209_at   up   0.006601   prostaglandin E receptor 1 (subtype EP1), 42 kDa       37337_at   down   0.006676   small nuclear ribonucleoprotein polypeptide G       2036_s_at   down   0.006697   CD44 antigen (homing function and Indian blood group                   system)       39168_at   up   0.00673   Ac-like transposable element       36229_at   up   0.006732   interleukin 17 receptor       39034_at   down   0.006748   DKFZP564O123 protein       39428_at   down   0.00676   lymphocyte adaptor protein       33181_at   down   0.006774   protein phosphatase 2 (formerly 2A), catalytic subunit,                   alpha isoform       40225_at   up   0.006775   cyclin G associated kinase       37939_at   up   0.006831   apolipoprotein B mRNA editing enzyme, catalytic                   polypeptide-like 3C       35814_at   down   0.006855   dendritic cell protein       40790_at   down   0.006931   basic helix-loop-helix domain containing, class B, 2       36779_at   up   0.006977   fatty acid binding protein 6, ileal (gastrotropin)       1525_s_at   up   0.006997   fibroblast growth factor 8 (androgen-induced)       34630_s_at   up   0.007011   dynein, axonemal, heavy polypeptide 9       40306_at   up   0.007012   v-raf murine sarcoma viral oncogene homolog B1       37731_at   down   0.007018   epidermal growth factor receptor pathway substrate 15       35512_at   up   0.007135       39926_at   down   0.007144   MAD, mothers against decapentaplegic homolog 5                   ( Drosophila )       34397_at   down   0.007213   acid-inducible phosphoprotein       39784_at   down   0.007234   eukaryotic translation initiation factor 2, subunit 1 alpha,                   35 kDa       39454_f_at   up   0.007249   T-cell leukemia, homeobox 2       35892_at   up   0.00729   complement component (3b/4b) receptor 1, including                   Knops blood group system       38848_at   up   0.007302   zymogen granule protein 16       2094_s_at   up   0.007347   v-fos FBJ murine osteosarcoma viral oncogene homolog       34559_at   up   0.007367       35643_at   down   0.007384   nucleobindin 2       40885_s_at   down   0.007411   syntaxin 16       40847_at   up   0.007437   flavoprotein oxidoreductase MICAL2       237_s_at   down   0.007442   protein phosphatase 2 (formerly 2A), catalytic subunit,                   alpha isoform       35286_r_at   down   0.007473   putative nucleic acid binding protein RY-1       518_at   up   0.007484   nuclear receptor subfamily 1, group H, member 2       162_at   up   0.007506   ubiquitin specific protease 11       38226_at   down   0.007549   hypothetical protein FLJ10569       32134_at   down   0.007574   testis derived transcript (3 LIM domains)       33385_g_at   down   0.0076   calpastatin       35716_at   up   0.007601   sulfotransferase family, cytosolic, 1C, member 1       38447_at   up   0.007604   adrenergic, beta, receptor kinase 1       38992_at   down   0.007658   DEK oncogene (DNA binding)       33889_s_at   up   0.007667   DiGeorge syndrome critical region gene 2       38162_at   up   0.007683   regulating synaptic membrane exocytosis 2       38707_r_at   up   0.007701   E2F transcription factor 4, p107/p130-binding       41212_r_at   down   0.007709   Williams-Beuren syndrome chromosome region 1       32740_at   down   0.007724   KIAA0941 protein       35246_at   up   0.007732   TYRO3 protein tyrosine kinase       32090_at   up   0.007747   nicotinamide nucleotide adenylyltransferase 2       35411_at   up   0.007824   chromosome 16 open reading frame 7       31957_r_at   up   0.007826   ribosomal protein, large, P1       38084_at   down   0.007858   chromobox homolog 3 (HP1 gamma homolog, Drosophil       39136_at   down   0.007923   oxidative-stress responsive 1       33727_r_at   up   0.007975   tumor necrosis factor receptor superfamily, member 6b,                   decoy       39160_at   down   0.007995   pyruvate dehydrogenase (lipoamide) beta       584_s_at   down   0.008042   X-ray repair complementing defective repair in Chinese                   hamster cells 5 (double-strand-break rejoining; Ku                   autoantigen, 80 kDa)       36317_at   up   0.008056   coronin, actin binding protein, 2A       32298_at   up   0.008057   a disintegrin and metalloproteinase domain 2 (fertilin bet       39714_at   down   0.008105   SH3 domain binding glutamic acid-rich protein like       36523_at   down   0.00813   ATPase, Cu++ transporting, alpha polypeptide (Menkes                   syndrome)       37411_at   up   0.008164   centaurin, beta 1       33247_at   down   0.008182   proteasome (prosome, macropain) 26S subunit, non-                   ATPase, 14       32836_at   up   0.008183   1-acylglycerol-3-phosphate O-acyltransferase 1                   (lysophosphatidic acid acyltransferase, alpha)       36473_at   up   0.008198   ubiquitin specific protease 20       1499_at   down   0.0082   farnesyltransferase, CAAX box, alpha       33633_at   up   0.008238   purinergic receptor P2Y, G-protein coupled, 11       38736_at   down   0.008238   WD repeat domain 1       31796_at   up   0.008255   kinesin family member 1C       36608_at   down   0.008257   malate dehydrogenase 1, NAD (soluble)       32725_at   down   0.008258   BH3 interacting domain death agonist       34615_at   up   0.008286   keratin 12 (Meesmann corneal dystrophy)       39517_at   down   0.008321   HTGN29 protein       34503_at   up   0.008323       37740_r_at   down   0.008356   solute carrier family 25 (mitochondrial carrier; adenine                   nucleotide translocator), member 5       39442_at   down   0.008385   unc-50 related       38395_at   down   0.00841   NADH dehydrogenase (ubiquinone) Fe—S protein 1,                   75 kDa (NADH-coenzyme Q reductase)       33336_at   up   0.008411   solute carrier family 4, anion exchanger, member 1                   (erythrocyte membrane protein band 3, Diego blood                   group)       35738_at   down   0.008416   high mobility group nucleosomal binding domain 4       39473_r_at   up   0.008426   protein tyrosine phosphatase type IVA, member 3       32070_at   up   0.008449   protein tyrosine phosphatase, receptor type, C-associat                   protein       36824_at   up   0.008494   astrotactin       35492_at   up   0.00852   cytochrome P450, family 4, subfamily F, polypeptide 12       40146_at   down   0.008529   RAP1B, member of RAS oncogene family       36660_at   down   0.00856   RAB11A, member RAS oncogene family       33791_at   up   0.008585   deleted in lymphocytic leukemia, 1       37475_at   up   0.008624   DKFZP434J046 protein       34480_at   up   0.008635   cadherin 16, KSP-cadherin       35278_at   up   0.008637   ribosomal protein S29       37720_at   down   0.008641   heat shock 60 kDa protein 1 (chaperonin)       35612_at   up   0.00866   DKFZP564P1916 protein       36090_at   down   0.0087   transducin (beta)-like 2       41722_at   down   0.008706   nicotinamide nucleotide transhydrogenase       1228_s_at   down   0.008746   meningioma expressed antigen 6 (coiled-coil proline-rich       34323_at   down   0.008748   thyroid receptor interacting protein 15       36975_at   down   0.00878   hypothetical protein MGC8721       875_g_at   up   0.008864   chemokine (C—C motif) ligand 2       1908_at   up   0.008924   ets variant gene 3       33665_s_at   down   0.00895   colony stimulating factor 2 receptor, alpha, low-affinity                   (granulocyte-macrophage)       37351_at   up   0.008972   uridine phosphorylase       38656_s_at   down   0.008989   hypothetical protein MGC5576       33845_at   down   0.00901   heterogeneous nuclear ribonucleoprotein H1 (H)       1187_at   up   0.009027   ligase III, DNA, ATP-dependent       31700_at   up   0.009079   G protein-coupled receptor 35       37166_at   up   0.009158   3-hydroxyanthranilate 3,4-dioxygenase       35521_at   up   0.009159   claudin 9       39384_at   up   0.009225   ELAV (embryonic lethal, abnormal vision,  Drosophila )-lik                   1 (Hu antigen R)       31495_at   up   0.009226   chemokine (C motif) ligand 2       1011_s_at   down   0.009274   tyrosine 3-monooxygenase/tryptophan 5-monooxygenas                   activation protein, epsilon polypeptide       33150_at   down   0.009294   disrupter of silencing 10       41118_at   up   0.009318   hypothetical protein FLJ13639       34370_at   down   0.009349   archain 1       AFFX-   down   0.009365   signal transducer and activator of transcription 1, 91 kDa       HUMISGF3A/M97935_3_at       32778_at   down   0.009367   inositol 1,4,5-triphosphate receptor, type 1       41223_at   down   0.009391   cytochrome c oxidase subunit Va       32452_at   up   0.009405   cyclin-dependent kinase 3       39326_at   up   0.009436   ATPase, H+ transporting, lysosomal V0 subunit a isoform 1       36264_at   up   0.00945   megakaryocyte-associated tyrosine kinase       35136_at   down   0.009509   nuclear transport factor 2-like export factor 2       34448_s_at   up   0.009565   caspase 2, apoptosis-related cysteine protease (neural                   precursor cell expressed, developmentally down-regulat                   2)       36012_at   down   0.00959   progesterone-induced blocking factor 1       39375_g_at   up   0.009636   G-2 and S-phase expressed 1       39023_at   down   0.009731   isocitrate dehydrogenase 1 (NADP+), soluble       41771_g_at   up   0.009755   monoamine oxidase A       37579_at   up   0.009808   cytoplasmic FMR1 interacting protein 2       36931_at   up   0.009886   transgelin       37328_at   down   0.009996   pleckstrin       38058_at   up   0.010002   dermatopontin       40802_at   down   0.010028   DKFZP434C212 protein       1675_at   down   0.010041   RAS p21 protein activator (GTPase activating protein) 1       35741_at   down   0.01005   phosphatidylinositol-4-phosphate 5-kinase, type II, beta       38046_at   down   0.01007   IK cytokine, down-regulator of HLA II       39686_g_at   down   0.010084   like mouse brain protein E46       850_r_at   up   0.010147   insulin receptor substrate 1       36152_at   up   0.010166   GDP dissociation inhibitor 1       40931_at   down   0.010287   CGI-100 protein       38375_at   down   0.010289   esterase D/formylglutathione hydrolase       31726_at   up   0.010328   gamma-aminobutyric acid (GABA) A receptor, alpha 3       33902_at   up   0.01033   glycerol-3-phosphate dehydrogenase 1 (soluble)       32749_s_at   up   0.010344   filamin A, alpha (actin binding protein 280)       33331_at   up   0.010358   BENE protein       35276_at   up   0.010366   claudin 4       34196_at   down   0.010443   ocular development-associated gene       1211_s_at   down   0.010444   CASP2 and RIPK1 domain containing adaptor with deat                   domain       133_at   down   0.010451   cathepsin C       41342_at   down   0.010536   RAN binding protein 1       39605_at   up   0.010552   forkhead box G1B       35412_at   up   0.010552   cytochrome P450, family 4, subfamily A, polypeptide 11       33645_at   up   0.01057   GM2 ganglioside activator protein       34778_at   up   0.010585       39281_at   up   0.010599   Rho guanine nucleotide exchange factor (GEF) 11       38676_at   down   0.010653   stress 70 protein chaperone, microsome-associated,                   60 kDa       37254_at   up   0.010656   zinc finger protein 133 (clone pHZ-13)       38631_at   down   0.010686   tumor necrosis factor, alpha-induced protein 2       33373_at   down   0.010724       32816_at   down   0.01074   small glutamine-rich tetratricopeptide repeat (TPR)-                   containing       567_s_at   up   0.01077   promyelocytic leukemia       34707_at   up   0.010772   chromodomain helicase DNA binding protein 3       34785_at   down   0.010772   KIAA1025 protein       AFFX-BioDn-   up   0.0108       3_at       34894_r_at   up   0.010828   protease, serine, 22       1787_at   down   0.010871   cyclin-dependent kinase inhibitor 1C (p57, Kip2)       35960_at   up   0.010922   inhibitor of kappa light polypeptide gene enhancer in B-                   cells, kinase beta       33679_f_at   up   0.010949   tubulin, beta, 2       33458_r_at   down   0.010981   histone 1, H2bc       32212_at   down   0.011004   programmed cell death 8 (apoptosis-inducing factor)       32210_at   up   0.011012   phosphoglucomutase 1       38976_at   up   0.011013   coronin, actin binding protein, 1A       41657_at   up   0.011105   serine/threonine kinase 11 (Peutz-Jeghers syndrome)       39760_at   down   0.011179   quaking homolog, KH domain RNA binding (mouse)       39592_r_at   down   0.011186   fibrinogen-like 2       38269_at   up   0.011209   protein kinase D2       39212_at   up   0.011221   hypothetical protein FLJ11191       41081_at   up   0.0113   BUB1 budding uninhibited by benzimidazoles 1 homolog                   (yeast)       36272_r_at   up   0.011309   peripheral myelin protein 2       36669_at   up   0.011328   FBJ murine osteosarcoma viral oncogene homolog B       40874_at   down   0.011345   endothelial differentiation-related factor 1       1877_g_at   down   0.011363       36886_f_at   up   0.011466   killer cell immunoglobulin-like receptor, two domains, Ion                   cytoplasmic tail, 3       36924_r_at   up   0.011516   secretogranin II (chromogranin C)       38439_at   up   0.011558   nuclear factor (erythroid-derived 2)-like 1       39733_at   down   0.011569   homocysteine-inducible, endoplasmic reticulum stress-                   inducible, ubiquitin-like domain member 1       33034_at   up   0.011597   rhomboid, veinlet-like 1 ( Drosophila )       32380_at   up   0.01161   plakophilin 1 (ectodermal dysplasia/skin fragility                   syndrome)       41819_at   down   0.011617   FYN binding protein (FYB-120/130)       781_at   down   0.011656   Rab geranylgeranyltransferase, beta subunit       37943_at   down   0.011657   zinc finger, FYVE domain containing 26       41641_at   up   0.011665   GPI-anchored metastasis-associated protein homolog       273_g_at   up   0.011718   gastrin-releasing peptide       36891_at   up   0.01173   putative acyltransferase       32235_at   up   0.011759   mahogunin, ring finger 1       33750_at   up   0.01177   protein tyrosine phosphatase, receptor type, U       2063_at   down   0.011827   excision repair cross-complementing rodent repair                   deficiency, complementation group 5 (xeroderma                   pigmentosum, complementation group G (Cockayne                   syndrome))       466_at   down   0.011856   general transcription factor II, i       38755_at   up   0.011889   Fas (TNFRSF6)-associated via death domain       37850_at   up   0.011942   hypothetical protein dJ462O23.2       36894_at   up   0.011976   plakophilin 4       38710_at   up   0.012032   ubiquitin-specific protease otubain 1       35165_at   down   0.012038   hypothetical protein MGC13033       37728_r_at   down   0.012091   reticulocalbin 2, EF-hand calcium binding domain       32837_at   up   0.0121   1-acylglycerol-3-phosphate O-acyltransferase 2                   (lysophosphatidic acid acyltransferase, beta)       1717_s_at   down   0.012108   baculoviral IAP repeat-containing 3       933_f_at   down   0.012134   zinc finger protein 91 (HPF7, HTF10)       37919_at   up   0.012214   solute carrier family 21 (prostaglandin transporter),                   member 2       1196_at   up   0.012219   chromosome condensation 1       1285_at   up   0.012233       41490_at   down   0.012323   phosphoribosyl pyrophosphate synthetase 2       504_at   down   0.012336   ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog,                   yeast)       34146_at   up   0.01236   8-oxoguanine DNA glycosylase       36336_s_at   up   0.012444   KIAA0963 protein       36198_at   down   0.012492   translocase of outer mitochondrial membrane 20 (yeast)                   homolog       32000_g_at   up   0.012498   ATP-binding cassette, sub-family A (ABC1), member 1       41257_at   down   0.012502   calpastatin       34768_at   down   0.012514   thioredoxin domain containing       31977_at   up   0.012525   guanylate cyclase 2D, membrane (retina-specific)       39628_at   up   0.012571   RAB9A, member RAS oncogene family       36583_at   down   0.012698   sorting nexin 1       41179_at   down   0.012738   ring finger protein 44       36436_at   up   0.012745   leukocyte cell-derived chemotaxin 2       39327_at   up   0.012808   Melanoma associated gene       31525_s_at   up   0.012813   hemoglobin, alpha 2       1815_g_at   down   0.012835   transforming growth factor, beta receptor II (70/80 kDa)       40745_at   up   0.012844   adaptor-related protein complex 1, beta 1 subunit       1795_g_at   up   0.012848   cyclin D3       1079_g_at   up   0.012852   prolactin receptor       40837_at   up   0.012862   transducin-like enhancer of split 2 (E(sp1) homolog,                     Drosophila )       34440_at   up   0.012898   DiGeorge syndrome critical region gene 9       33433_at   down   0.012905   DKFZP564F0522 protein       40613_at   down   0.012921   chromosome 6 open reading frame 62       40182_s_at   up   0.012959   coactivator-associated arginine methyltransferase-1       36425_at   up   0.012979   nebulette       31995_g_at   up   0.012992   ADP-ribosylation factor guanine nucleotide-exchange                   factor 2 (brefeldin A-inhibited)       36338_at   up   0.013004   leucine zipper protein 1       34753_at   down   0.013079   synaptobrevin-like 1       41036_at   up   0.01309   hypothetical protein FLJ12242       33568_at   up   0.013116   cholinergic receptor, nicotinic, beta polypeptide 4       36550_at   down   0.013154   Ras and Rab interactor 2       35564_at   up   0.013202       34334_at   up   0.013236   ephrin-B2       35848_at   down   0.013256   retinoic acid induced 17       33264_at   up   0.013299   rTS beta protein       41080_at   up   0.013323   H2A histone family, member B       40130_at   up   0.013335   follistatin-like 1       32233_at   down   0.013347   torsin family 1, member B (torsin B)       35209_at   down   0.013359   EPM2A (laforin) interacting protein 1       40644_g_at   up   0.013371   integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa                   complex, antigen CD41B)       41063_g_at   up   0.013386   likely ortholog of mouse nervous system polycomb 1       37747_at   down   0.013389   annexin A5       31599_f_at   up   0.013395   melanoma antigen, family A, 6       39140_at   down   0.013426   nucleic acid helicase DDXx       41634_at   down   0.013478   KIAA0256 gene product       1789_at   down   0.013483   COP9 constitutive photomorphogenic homolog subunit 5                   ( Arabidopsis )       34385_at   down   0.013542   succinate dehydrogenase complex, subunit C, integral                   membrane protein, 15 kDa       39955_at   up   0.013562   deleted in lymphocytic leukemia, 2       1147_at   up   0.013573       40539_at   up   0.013587   myosin IXB       36472_at   down   0.013625   N-myc (and STAT) interactor       40783_s_at   up   0.013679   phosphatidylinositol 4-kinase, catalytic, alpha polypeptid       36171_at   down   0.013705   activated RNA polymerase II transcription cofactor 4       35868_at   up   0.013726   advanced glycosylation end product-specific receptor       1245_i_at   down   0.013758   p21 (CDKN1A)-activated kinase 2       37793_r_at   up   0.013825   RAD51-like 3 ( S. cerevisiae )       35082_at   up   0.013847   Zic family member 3 heterotaxy 1 (odd-paired homolog,                     Drosophila )       34762_at   up   0.013858   ring finger protein (C3HC4 type) 8       41187_at   down   0.013902   myosin regulatory light chain MRLC2       33879_at   up   0.013908   type I sigma receptor       1652_at   up   0.013938   pim-2 oncogene       40417_at   down   0.013938   chaperonin containing TCP1, subunit 5 (epsilon)       41129_at   down   0.013943   KIAA0033 protein       38420_at   up   0.013954   collagen, type V, alpha 2       34210_at   down   0.014015   CDW52 antigen (CAMPATH-1 antigen)       39344_at   down   0.014023   transformer-2 alpha (htra-2 alpha)       1706_at   up   0.014079   v-raf murine sarcoma 3611 viral oncogene homolog 1       34661_at   up   0.014103   KIAA0350 protein       38993_r_at   down   0.014129       32184_at   down   0.014139   LIM domain only 2 (rhombotin-like 1)       36631_at   down   0.014147   peroxiredoxin 3       35371_at   up   0.014173   LPS-responsive vesicle trafficking, beach and anchor                   containing       39640_at   up   0.014174   glutamine-fructose-6-phosphate transaminase 2       36019_at   up   0.014196   serine/threonine kinase 19       37584_at   up   0.014203   Fanconi anemia, complementation group G       36011_at   up   0.014257   syntaxin 10       36482_s_at   up   0.014257   ATPase, Ca++ transporting, ubiquitous       31950_at   down   0.014258   poly(A) binding protein, cytoplasmic 1       37220_at   down   0.014462   Fc fragment of IgG, high affinity Ia, receptor for (CD64)       37121_at   up   0.014557   natural killer cell group 7 sequence       36538_at   up   0.014685   protein phosphatase 1, regulatory (inhibitor) subunit 13B       38686_at   up   0.014734   ATPase, H+ transporting, lysosomal 38 kDa, V0 subunit                   isoform 1       32695_at   down   0.014748   HIV TAT specific factor 1       32121_at   down   0.014803   phosphoinositide-3-kinase, catalytic, delta polypeptide       37374_at   down   0.014809   annexin A4       41273_at   up   0.014835   FK506 binding protein 12-rapamycin associated protein       32464_at   up   0.014865   defensin, beta 4       34293_at   up   0.014917   kinesin family member C3       37035_at   down   0.014931   stress-associated endoplasmic reticulum protein 1       1318_at   down   0.014941   retinoblastoma binding protein 4       35215_at   down   0.014941   HDCMA18P protein       38572_at   up   0.01496   FGFR1 oncogene partner       32258_r_at   down   0.014963   telomeric repeat binding factor (NIMA-interacting) 1       34646_at   down   0.014971   ribosomal protein S7       33821_at   down   0.014993   homolog of yeast long chain polyunsaturated fatty acid                   elongation enzyme 2       37038_at   down   0.015036   ATP-binding cassette, sub-family D (ALD), member 3       38463_s_at   down   0.015059   adenosine monophosphate deaminase (isoform E)       31668_f_at   up   0.015097   erythrocyte membrane protein band 4.1-like 2       34310_at   up   0.015109   adenine phosphoribosyltransferase       1324_at   up   0.015162   RAD9 homolog ( S. pombe )       40989_at   up   0.01517   tetraspan 5       32493_at   up   0.015183   thyrotrophic embryonic factor       39694_at   up   0.015198   hypothetical protein MGC5508       34763_at   down   0.015201   chondroitin sulfate proteoglycan 6 (bamacan)       41134_at   up   0.015209   disks large-associated protein 4       36136_at   up   0.015225   tumor protein p53 inducible protein 11       35973_at   down   0.015225   huntingtin interacting protein 14       36004_at   up   0.015262   inhibitor of kappa light polypeptide gene enhancer in B-                   cells, kinase gamma       37506_at   down   0.01527   formin binding protein 3       36795_at   up   0.015294   prosaposin (variant Gaucher disease and variant                   metachromatic leukodystrophy)       31808_at   down   0.015332   inhibitor of growth family, member 3       38829_r_at   down   0.015403   KH-type splicing regulatory protein (FUSE binding protein                   2)       34301_r_at   up   0.015458   keratin 17       39392_at   down   0.01557   glyceronephosphate O-acyltransferase       41132_r_at   down   0.015577   heterogeneous nuclear ribonucleoprotein H2 (H′)       35952_at   up   0.015587       31882_at   up   0.015605   RNA, U3 small nucleolar interacting protein 2       40132_g_at   down   0.015651   follistatin-like 1       31999_at   up   0.01568   ATP-binding cassette, sub-family A (ABC1), member 1       32214_at   down   0.015754   thioredoxin-like, 32 kDa       38244_at   up   0.015774   hypothetical protein FLJ10178       38841_at   down   0.01586   putative glialblastoma cell differentiation-related       40615_at   down   0.015863   hypothetical protein FLJ21439       36932_at   down   0.015868   general transcription factor IIIC, polypeptide 2, beta                   110 kDa       40684_at   up   0.015914   GTP cyclohydrolase I feedback regulatory protein       537_f_at   up   0.015947   breakpoint cluster region       40246_at   down   0.015992   discs, large ( Drosophila ) homolog 1       31924_at   up   0.016021   testicular soluble adenylyl cyclase       952_at   down   0.016057       33925_at   up   0.016064   neurogranin (protein kinase C substrate, RC3)       41784_at   down   0.016071   SR rich protein       32696_at   down   0.016102   pre-B-cell leukemia transcription factor 3       39857_at   down   0.016137   syntaxin 11       33186_i_at   up   0.01614       33297_at   down   0.016149   chromosome 6 open reading frame 130       872_i_at   up   0.016203   insulin receptor substrate 1       35080_at   up   0.016227   neurotensin receptor 1 (high affinity)       40933_f_at   up   0.016236   zinc finger, DHHC domain containing 18       38380_at   down   0.016279   POP4 (processing of precursor,  S. cerevisiae ) homolog       34962_at   up   0.01628       40203_at   down   0.016313   putative translation initiation factor       31511_at   up   0.016334   ribosomal protein S9       821_s_at   down   0.016432   folate receptor 1 (adult)       37973_at   down   0.016448   sorting nexin 13       229_at   down   0.01645   CCAAT-box-binding transcription factor       1159_at   up   0.016461   interleukin 7       343_s_at   up   0.016526   ectonucleotide pyrophosphatase/phosphodiesterase 1       40315_at   up   0.016527   serine protease inhibitor, Kazal type, 5       34813_at   down   0.016531   eukaryotic translation initiation factor 1A       38868_at   up   0.01656   Fc fragment of IgA, receptor for       1601_s_at   down   0.016625   insulin-like growth factor binding protein 5       40189_at   down   0.016702   SET translocation (myeloid leukemia-associated)       34679_at   up   0.016704   breakpoint cluster region       35915_at   up   0.01671   inhibin, beta C       40619_at   up   0.016734   ubiquitin carrier protein       39740_g_at   down   0.016741   nascent-polypeptide-associated complex alpha                   polypeptide       38016_at   down   0.016744   heterogeneous nuclear ribonucleoprotein D (AU-rich                   element RNA binding protein 1, 37 kDa)       1707_g_at   up   0.01675   v-raf murine sarcoma 3611 viral oncogene homolog 1       41459_at   down   0.016767   tripeptidyl peptidase II       41524_at   down   0.01681   inositol polyphosphate-1-phosphatase       41085_at   up   0.016818   polymerase (DNA directed), epsilon 2 (p59 subunit)       155_s_at   down   0.016819   ubiquitin-like 1 (sentrin)       1650_g_at   up   0.016871   chromosome 20 open reading frame 16       41059_at   down   0.016883   leukocyte membrane antigen       32700_at   down   0.016939   guanylate binding protein 2, interferon-inducible       41749_at   down   0.01696   chromosome 21 open reading frame 33       33603_at   up   0.016974   ATP-binding cassette, sub-family D (ALD), member 1       36159_s_at   down   0.017029   prion protein (p27-30) (Creutzfeld-Jakob disease,                   Gerstmann-Strausler-Scheinker syndrome, fatal familial                   insomnia)       37843_i_at   up   0.017095   class I cytokine receptor       1555_f_at   up   0.017101   cytochrome P450, family 2, subfamily A, polypeptide 7       36445_at   up   0.017109   chemokine (C—C motif) ligand 23       37449_i_at   up   0.017262   GNAS complex locus       31613_at   up   0.017304   laminin, beta 4       31746_at   up   0.017309   zinc finger protein 204       37962_r_at   down   0.017344   syntaxin binding protein 3       2044_s_at   down   0.017376   retinoblastoma 1 (including osteosarcoma)       35327_at   down   0.017394   eukaryotic translation initiation factor 3, subunit 3 gamma                   40 kDa       34730_g_at   up   0.017407   trophinin       31406_at   up   0.017412   G protein-coupled receptor 50       31932_f_at   down   0.017423   basic transcription factor 3       442_at   down   0.017431   tumor rejection antigen (gp96) 1       151_s_at   up   0.017469   hypothetical protein DKFZp434N0650       40817_at   up   0.017498   nucleobindin 1       34637_f_at   up   0.017511   alcohol dehydrogenase 1A (class I), alpha polypeptide       32350_at   down   0.017517   mucosa associated lymphoid tissue lymphoma                   translocation gene 1       33778_at   up   0.017561   chromosome 22 open reading frame 4       31687_f_at   up   0.017608   hemoglobin, beta       AFFX-BioC-3_at   up   0.017611       1420_s_at   down   0.017633   eukaryotic translation initiation factor 4A, isoform 2       33441_at   up   0.017697   T-cell leukemia translocation altered gene       37871_at   up   0.017737   islet amyloid polypeptide       32971_at   up   0.017788   Friedreich ataxia region gene X123       39547_at   up   0.017849   RAN binding protein 9       37727_i_at   down   0.017866   reticulocalbin 2, EF-hand calcium binding domain       33467_at   up   0.017871   CMRF35 leukocyte immunoglobulin-like receptor       32287_s_at   up   0.017884   killer cell lectin-like receptor subfamily C, member 3       1903_at   down   0.017927       36195_at   down   0.018011   isocitrate dehydrogenase 3 (NAD+) alpha       40609_at   up   0.018045   helicase with SNF2 domain 1       32599_at   down   0.018087   tuberous sclerosis 1       37015_at   down   0.018105   aldehyde dehydrogenase 1 family, member A1       36590_at   up   0.018149   solute carrier family 16 (monocarboxylic acid                   transporters), member 2 (putative transporter)       38830_at   up   0.018172   hypothetical protein FLJ11198       1986_at   down   0.018179   retinoblastoma-like 2 (p130)       192_at   down   0.018213   TAF7 RNA polymerase II, TATA box binding protein                   (TBP)-associated factor, 55 kDa       35630_at   up   0.018226   lethal giant larvae homolog 2 ( Drosophila )       40637_at   down   0.018269   heat shock 70 kDa protein 8       31768_at   up   0.018276   histone 1, H2ai       34253_at   down   0.018328   nucleoporin 160 kDa       36783_f_at   down   0.018333   Krueppel-related zinc finger protein       31914_at   up   0.018338   chromodomain helicase DNA binding protein 1-like       41374_at   up   0.0184   ribosomal protein S6 kinase, 70 kDa, polypeptide 2       40754_at   up   0.018431   general transcription factor IIH, polypeptide 3, 34 kDa       34857_at   down   0.018445   hypothetical protein FLJ20986       33534_at   up   0.018485   endothelial cell-specific molecule 1       41852_at   up   0.018525   rearranged L-myc fusion sequence       32181_at   up   0.018613   fiotillin 2       37967_at   up   0.01865   leukocyte specific transcript 1       33084_at   up   0.018756   complexin 2       32345_at   up   0.018764       1295_at   down   0.018786   v-rel reticuloendotheliosis viral oncogene homolog A,                   nuclear factor of kappa light polypeptide gene enhancer                   B-cells 3, p65 (avian)       40166_at   down   0.01879   likely ortholog of mouse WD-40-repeat-containing protein                   with a SOCS box 2       38068_at   down   0.018828   autocrine motility factor receptor       1038_s_at   down   0.018932   interferon gamma receptor 1       41601_at   down   0.018953   a disintegrin and metalloproteinase domain 17 (tumor                   necrosis factor, alpha, converting enzyme)       2057_g_at   up   0.018958   fibroblast growth factor receptor 1 (fms-related tyrosine                   kinase 2, Pfeiffer syndrome)       226_at   down   0.018995   protein kinase, cAMP-dependent, regulatory, type I, alph                   (tissue specific extinguisher 1)       32850_at   down   0.018999   nucleoporin 153 kDa       36186_at   up   0.01902   RNA binding protein S1, serine-rich domain       34644_at   up   0.019096   beta-2-microglobulin       300_f_at   down   0.019103       825_at   down   0.019195   PRP4 pre-mRNA processing factor 4 homolog B (yeast)       35938_at   down   0.019217   phospholipase A2, group IVA (cytosolic, calcium-                   dependent)       36539_at   up   0.019221   immunoglobulin lambda locus       34086_at   up   0.019292   endothelial differentiation, sphingolipid G-protein-couple                   receptor, 5       34525_at   up   0.019298   T-cell leukemia/lymphoma 1B       38007_at   up   0.019318   neurofibromin 2 (bilateral acoustic neuroma)       36463_at   down   0.019332   BCL2-associated athanogene 5       33109_f_at   up   0.019346   SRY (sex determining region Y)-box 2       40309_at   up   0.019388   carbonic anhydrase IX       34349_at   down   0.019479   SEC63-like ( S. cerevisiae )       691_g_at   up   0.019503   procollagen-proline, 2-oxoglutarate 4-dioxygenase (proli                   4-hydroxylase), beta polypeptide (protein disulfide                   isomerase; thyroid hormone binding protein p55)       38657_s_at   up   0.019523   clathrin, light polypeptide (Lca)       40365_at   up   0.019556   guanine nucleotide binding protein (G protein), alpha 15                   (Gq class)       36576_at   down   0.019565   H2A histone family, member Y       2004_at   down   0.019576   mitogen-activated protein kinase kinase kinase 1       31890_s_at   down   0.019638   zinc finger protein 143 (clone pHZ-1)       510_g_at   down   0.019641   MAD, mothers against decapentaplegic homolog 4                   ( Drosophila )       32183_at   down   0.01973   splicing factor, arginine/serine-rich 11       37812_at   up   0.019731   cut-like 2 ( Drosophila )       41131_f_at   down   0.019743   heterogeneous nuclear ribonucleoprotein H2 (H′)       32265_at   up   0.019747   nuclear receptor subfamily 4, group A, member 1       33771_at   up   0.019763   T-cell activation leucine repeat-rich protein       531_at   down   0.019841   GLI pathogenesis-related 1 (glioma)       34796_at   down   0.01992   translocation associated membrane protein 1       35312_at   up   0.019979   MCM2 minichromosome maintenance deficient 2, mitoti                   ( S. cerevisiae )       35303_at   down   0.020035   insulin induced gene 1       36547_r_at   up   0.020045   KIAA0542 gene product       35650_at   down   0.020047   KIAA0356 gene product       34387_at   down   0.020082   KIAA0205 gene product       40208_at   up   0.020123   growth differentiation factor 11       41147_at   down   0.020124   hypothetical protein MGC4276 similar to CG8198       32171_at   down   0.020139   eukaryotic translation initiation factor 5       35798_at   up   0.020169   NS1-associated protein 1       39657_at   up   0.02024   keratin 4       34147_g_at   up   0.02024   8-oxoguanine DNA glycosylase       41195_at   down   0.020265   LIM domain containing preferred translocation partner in                   lipoma       36514_at   down   0.02029   cell growth regulatory with ring finger domain       39833_at   up   0.020298   misshapen/NIK-related kinase       38717_at   down   0.02043   DKFZP586A0522 protein       34884_at   up   0.020442   carbamoyl-phosphate synthetase 1, mitochondrial       35674_at   down   0.020444   peptidyl arginine deiminase, type II       930_at   up   0.020469   protein phosphatase 2 (formerly 2A), regulatory subunit                   B″, alpha       40141_at   down   0.020498   cullin 4B       35012_at   down   0.020538   myeloid cell nuclear differentiation antigen       31326_at   up   0.020632       38088_r_at   up   0.020721   S100 calcium binding protein A4 (calcium protein,                   calvasculin, metastasin, murine placental homolog)       41335_at   down   0.020743   DKFZP566O1646 protein       35048_at   up   0.020747   glutamate receptor, ionotrophic, AMPA 3       37545_at   up   0.020815   secretory carrier membrane protein 5       39750_at   up   0.020847   zinc finger, DHHC domain containing 3       37811_at   up   0.020897   calcium channel, voltage-dependent, alpha 2/delta subu 2       31728_at   up   0.02093   major histocompatibility complex, class II, DO alpha       39178_at   down   0.020932   reticulon 1       40636_at   up   0.020943   fiotillin 1       1062_g_at   down   0.02097   interleukin 10 receptor, alpha       39400_at   up   0.020978   KIAA1055 protein       34383_at   down   0.021052   ubiquitin specific protease 1       39793_at   down   0.021068   glioblastoma amplified sequence       36934_at   down   0.021189   chromosome 20 open reading frame 111       38815_at   down   0.021221   actin related protein 2/3 complex, subunit 1A, 41 kDa       38780_at   down   0.021235   aldo-keto reductase family 1, member A1 (aldehyde                   reductase)       38685_at   down   0.021249   syntaxin 12       34751_at   down   0.021264   zinc finger and BTB domain containing 1       39108_at   up   0.021289   lanosterol synthase (2,3-oxidosqualene-lanosterol                   cyclase)       33908_at   up   0.02134   calpain 1, (mu/l) large subunit       32895_f_at   up   0.021352   HIV-1 Rev binding protein-like       37409_at   down   0.021533   SFRS protein kinase 2       32575_at   up   0.021556   nucleosome assembly protein 1-like 4       _at   down   0.0216   mucosa associated lymphoid tissue lymphoma                   translocation gene 1       36952_at   up   0.021656   hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-                   Coenzyme A thiolase/enoyl-Coenzyme A hydratase                   (trifunctional protein), alpha subunit       34767_at   down   0.021706   modulator of apoptosis 1       AFFX-   up   0.021712   glyceraldehyde-3-phosphate dehydrogenase       HUMGAPDH/M33197_M_st       352_at   up   0.021712   phosphotidylinositol transfer protein       38383_at   down   0.021745   5-methyltetrahydrofolate-homocysteine methyltransferas       36648_at   down   0.021783   cofactor required for Sp1 transcriptional activation, subur                   9, 33 kDa       40431_at   down   0.021788   KIAA0431 protein       36433_at   up   0.021793   glycine receptor, alpha 3       35918_at   up   0.021822   deleted in lung and esophageal cancer 1       37078_at   up   0.021832   CD3Z antigen, zeta polypeptide (TiT3 complex)       33278_at   up   0.021853   SA hypertension-associated homolog (rat)       39839_at   down   0.021855   cold shock domain protein A       39088_at   up   0.021896   seven transmembrane domain protein       35036_at   down   0.02195   complement component 1, q subcomponent, receptor 1       33382_at   down   0.021991   N-acylsphingosine amidohydrolase (acid ceramidase)-lik       41520_at   up   0.022029   hypothetical protein LOC284352       32563_at   down   0.022071   ATPase, Na+/K+ transporting, beta 3 polypeptide       40457_at   down   0.022156   splicing factor, arginine/serine-rich 3       36404_at   up   0.022162   glucagon-like peptide 1 receptor       893_at   up   0.022233   ubiquitin carrier protein       37691_at   up   0.0223   MADS box transcription enhancer factor 2, polypeptide B                   (myocyte enhancer factor 2B)       36191_at   down   0.022333   transcription factor A, mitochondrial       40801_at   down   0.022358   DKFZP434C212 protein       32953_at   up   0.022369   CD5 antigen (p56-62)       35450_s_at   up   0.022389   general transcription factor II, i       41726_at   up   0.022435   endothelin converting enzyme 1       37463_r_at   up   0.022459   splicing factor 3a, subunit 2, 66 kDa       37622_r_at   down   0.022516   PC4 and SFRS1 interacting protein 2       263_g_at   down   0.022574   adenosylmethionine decarboxylase 1       34400_at   down   0.022648   low molecular mass ubiquinone-binding protein (9.5 kD)       39501_f_at   up   0.022704   amyloid beta (A4) precursor protein-binding, family A,                   member 2 binding protein       2032_s_at   up   0.022708   integrin, alpha V (vitronectin receptor, alpha polypeptide,                   antigen CD51)       31879_at   down   0.022724   far upstream element (FUSE) binding protein 3       20 _at   down   0.022731   integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA·                   4 receptor)       41185_f_at   down   0.022767   SMT3 suppressor of mif two 3 homolog 2 (yeast)       41829_at   up   0.022808   likely ortholog of mouse la related protein       41388_at   up   0.022831   Meis1, myeloid ecotropic viral integration site 1 homolog                   (mouse)       38401_s_at   up   0.022852   DKFZP434D1335 protein       452_at   down   0.022861   SWI/SNF related, matrix associated, actin dependent                   regulator of chromatin, subfamily c, member 1       1649_at   up   0.022875   chromosome 20 open reading frame 16       38106_at   down   0.022878   TGF beta-inducible nuclear protein 1       34704_r_at   up   0.022898   chorionic somatomammotropin hormone 2       1388_g_at   down   0.022922   vitamin D (1,25-dihydroxyvitamin D3) receptor       35432_at   down   0.022924   mediator of RNA polymerase II transcription, subunit 6                   homolog (yeast)       AFFX-   up   0.022931   actin, beta       HSAC07/X00351_3_at       37493_at   down   0.023078   colony stimulating factor 2 receptor, beta, low-affinity                   (granulocyte-macrophage)       32646_at   up   0.023083   KIAA0449 protein       32001_s_at   up   0.023099   paired basic amino acid cleaving system 4       886_at   down   0.023115   deoxycytidine kinase       32858_at   up   0.023123   ubinuclein 1       707_s_at   up   0.023162       38791_at   up   0.02319   dolichyl-diphosphooligosaccharide-protein                   glycosyltransferase       40579_at   down   0.023229   HIV-1 Rev binding protein       41214_at   down   0.023253   ribosomal protein S4, Y-linked       37393_at   down   0.02326   hairy and enhancer of split 1, ( Drosophila )       35487_at   up   0.023272   bromodomain, testis-specific       32866_at   up   0.023293   KIAA0605 gene product       34773_at   down   0.023349   tubulin-specific chaperone a       32669_at   down   0.023384   suppressor of cytokine signaling 5       37697_s_at   down   0.023475   voltage-dependent anion channel 2       39809_at   down   0.023498   HMG-box containing protein 1       33268_at   up   0.023524   Smcx homolog, X chromosome (mouse)       33320_at   down   0.023552   MHC class I region ORF       32297_s_at   up   0.023584   killer cell lectin-like receptor subfamily C, member 2       34059_at   up   0.023596   Pvt1 oncogene homolog, MYC activator (mouse)       38732_at   down   0.023596   chloride channel, nucleotide-sensitive, 1A       41716_at   down   0.023639   rabconnectin-3       172_at   up   0.023662   inositol polyphosphate-5-phosphatase, 145 kDa       40361_at   up   0.023669   chaperonin containing TCP1, subunit 6B (zeta 2)       38693_at   down   0.02374   ATP synthase, H+ transporting, mitochondrial F0 comple;                   subunit g       40108_at   down   0.02382   basic leucine zipper and W2 domains 1       34306_at   down   0.023824   muscleblind-like ( Drosophila )       34967_at   up   0.02384   similar to RNA polymerase I transcription factor RRN3       40363_r_at   up   0.023842   nuclear factor of kappa light polypeptide gene enhancer                   B-cells 2 (p49/p100)       32264_at   up   0.023943   granzyme M (lymphocyte met-ase 1)       34084_at   up   0.023985   aldo-keto reductase family 1, member D1 (delta 4-3-                   ketosteroid-5-beta-reductase)       39742_at   down   0.024012   TRAF family member-associated NFKB activator       33298_at   down   0.024013   striatin, calmodulin binding protein       37819_at   down   0.024063   nuclear protein double minute 1       33389_at   down   0.024066   cytochrome P450, family 51, subfamily A, polypeptide 1       39905_i_at   down   0.024139   ADP-ribosylation factor GTPase activating protein 3       32782_r_at   up   0.024141   bullous pemphigoid antigen 1, 230/240 kDa       36369_at   up   0.024193   polymerase I and transcript release factor       335_r_at   up   0.024272       37094_at   up   0.024294   X-ray repair complementing defective repair in Chinese                   hamster cells 3       33854_at   down   0.0243   ATPase, H+ transporting, lysosomal 34 kDa, V1 subunit D       37651_at   down   0.024336   REST corepressor       32989_at   up   0.024341   regulatory factor X, 1 (influences HLA class II expression)       40536_f_at   up   0.024357   translation initiation factor IF2       38981_at   down   0.024383   NADH dehydrogenase (ubiquinone) 1 beta subcomplex,                   3, 12 kDa       325_s_at   up   0.024407       41574_at   down   0.024445   pinin, desmosome associated protein       41865_at   down   0.024447   ATP synthase mitochondrial F1 complex assembly factor 2       40275_at   up   0.024455   karyopherin alpha 6 (importin alpha 7)       40971_at   down   0.024476   ankyrin repeat and SAM domain containing 1       39868_at   up   0.024556   poly(rC) binding protein 3       37284_at   up   0.024592   sema domain, immunoglobulin domain (Ig),                   transmembrane domain (TM) and short cytoplasmic                   domain, (semaphorin) 4D       33994_g_at   up   0.024774   myosin, light polypeptide 6, alkali, smooth muscle and                   non-muscle       32705_at   up   0.024783   cytochrome P450, family 3, subfamily A, polypeptide 7       1757_i_at   up   0.024825   cytochrome P450, family 3, subfamily A, polypeptide 7       35199_at   down   0.024877   KIAA0982 protein       31468_f_at   up   0.024961   glutamate receptor, metabotropic 1       36372_at   up   0.02499   hexokinase 3 (white cell)       41082_at   up   0.024994   ras homolog gene family, member N       32110_at   down   0.025003   KIAA0523 protein       32162_r_at   up   0.025004       39746_at   down   0.025006   polymerase (RNA) II (DNA directed) polypeptide B,                   140 kDa       39598_at   up   0.025046   gap junction protein, beta 1, 32 kDa (connexin 32,                   Charcot-Marie-Tooth neuropathy, X-linked)       33815_at   down   0.025072   uridine monophosphate synthetase (orotate                   phosphoribosyl transferase and orotidine-5′-                   decarboxylase)       1315_at   up   0.025082   ornithine decarboxylase antizyme 1       33368_at   down   0.025136   protease, serine, 15       33312_at   down   0.025138   crystallin, alpha A       922_at   up   0.025139   protein phosphatase 2 (formerly 2A), regulatory subunit,                   (PR 65), alpha isoform       33234_at   down   0.02522   KIAA0117 protein       39383_at   up   0.025256   adenylate cyclase 6       36375_at   up   0.025313   outer dense fiber of sperm tails 1       32039_at   down   0.025325   adaptor-related protein complex 3, beta 1 subunit       1397_at   down   0.025353   mitogen-activated protein kinase kinase kinase 11       36599_at   down   0.02539   malic enzyme 2, NAD(+)-dependent, mitochondrial       39316_at   up   0.025404   RAB40C, member RAS oncogene family       41194_at   down   0.025416   signal recognition particle 14 kDa (homologous Alu RNA                   binding protein)       41088_at   down   0.02547   abhydrolase domain containing 2       38869_at   up   0.025484   KIAA1069 protein       33885_at   down   0.025514   KIAA0907 protein       32955_at   down   0.025531   hypothetical protein HSPC132       36670_at   up   0.025564   autoantigen       33630_s_at   up   0.025599   spectrin, beta, non-erythrocytic 2       36930_at   down   0.02563   nucleolar GTPase       33459_at   up   0.025662       40121_at   down   0.02568   huntingtin interacting protein 2       37562_at   up   0.025703   protocadherin 1 (cadherin-like 1)       37658_at   up   0.025706   growth arrest-specific 6       32880_at   up   0.02574   secretoglobin, family 1D, member 2       40094_r_at   up   0.025791   Lutheran blood group (Auberger b antigen included)       1849_s_at   down   0.025971   retinoblastoma binding protein 1       34342_s_at   up   0.025976   secreted phosphoprotein 1 (osteopontin, bone sialoprote                   I, early T-lymphocyte activation 1)       39679_at   up   0.025985   aquaporin 2 (collecting duct)       41133_at   down   0.02604   Ras-GTPase-activating protein SH3-domain-binding                   protein       40718_at   up   0.026084   cathepsin W (lymphopain)       _ _at   up   0.0261   galanin receptor 3       40029_at   up   0.026123   EGF-like-domain, multiple 3       41239_r_at   down   0.026185   cathepsin S       33363_at   up   0.026322   JTV1 gene       40980_at   up   0.026323   helicase with SNF2 domain 1       37280_at   up   0.026356   MAD, mothers against decapentaplegic homolog 1                   ( Drosophila )       37059_at   up   0.026359   glucokinase (hexokinase 4) regulatory protein       34304_s_at   down   0.02639   spermidine/spermine N1-acetyltransferase       41750_at   down   0.026432   protein disulfide isomerase-related protein       34026_at   up   0.026444       35828_at   up   0.026456   cysteine-rich protein 2       34655_at   up   0.02651   membrane protein, palmitoylated 2 (MAGUK p55                   subfamily member 2)       35955_at   up   0.026544   cytochrome c-like antigen       33930_at   down   0.026608   chromosome 14 open reading frame 163       40664_at   up   0.026615   brain-specific angiogenesis inhibitor 3       34110_g_at   up   0.026639   proline dehydrogenase (oxidase) 1       36271_at   up   0.026668   KIAA1024 protein       1498_at   up   0.026683   zeta-chain (TCR) associated protein kinase 70 kDa       1647_at   down   0.026835   IQ motif containing GTPase activating protein 2       35069_at   up   0.026876   hypothetical protein similar to preferentially expressed                   antigen of melanoma       35135_at   down   0.026898   hypothetical protein MGC10471       34099_f_at   down   0.02691   nucleosome assembly protein 1-like 1       33861_at   down   0.02691   CCR4-NOT transcription complex, subunit 2       39720_g_at   up   0.026932   zona pellucida glycoprotein 3 (sperm receptor)       249_at   up   0.026938   nuclear factor of activated T-cells, cytoplasmic,                   calcineurin-dependent 4       35013_at   up   0.026947   lipopolysaccharide binding protein       40164_at   up   0.027001   Rho GDP dissociation inhibitor (GDI) alpha       41828_at   down   0.027034   methyl-CpG binding domain protein 1       33658_at   down   0.027078   zinc finger protein 124 (HZF-16)       32665_at   down   0.027087   protein phosphatase 1B (formerly 2C), magnesium-                   dependent, beta isoform       35734_at   down   0.027114   ARP2 actin-related protein 2 homolog (yeast)       36753_at   down   0.027141   leukocyte immunoglobulin-like receptor, subfamily B (with                   TM and ITIM domains), member 4       35087_at   down   0.027142       34887_at   down   0.027168   radixin       36048_at   down   0.027245   zinc finger protein 318       728_at   up   0.027264       33030_at   up   0.027277   histone 1, H1d       35818_at   down   0.027352   cytochrome c, somatic       1171_s_at   up   0.027371       32508_at   down   0.027482   HBxAg transactivated protein 2       37758_s_at   up   0.027495   transcription factor Dp-1       31474_r_at   down   0.027515   tankyrase, TRF1-interacting ankyrin-related ADP-ribose                   polymerase       31716_at   up   0.027701   protocadherin 1 (cadherin-like 1)       39377_at   down   0.027712   mitochondrial ribosomal protein S27       32833_at   down   0.027752   CDC-like kinase 1       36702_at   up   0.027768   T-box 19       222_at   up   0.027825   exostoses (multiple) 1       35378_at   up   0.027861   luteinizing hormone beta polypeptide       37399_at   up   0.027864   aldo-keto reductase family 1, member C3 (3-alpha                   hydroxysteroid dehydrogenase, type II)       41249_at   down   0.027899   NAD kinase       37419_g_at   up   0.027936   POU domain, class 2, transcription factor 2       36598_s_at   up   0.028084   inositol polyphosphate phosphatase-like 1       36400_at   up   0.028084       34946_at   down   0.028102   immunoglobulin superfamily, member 6       39568_g_at   up   0.028143   aquaporin 7       33847_s_at   down   0.028151   cyclin-dependent kinase inhibitor 1B (p27, Kip1)       33774_at   down   0.028182   caspase 8, apoptosis-related cysteine protease       723_s_at   down   0.028219       40852_at   down   0.028237   tudor repeat associator with PCTAIRE 2       32315_at   down   0.02827   ribosomal protein S24       32017_at   up   0.028338   par-6 partitioning defective 6 homolog beta ( C. elegans )       32254_at   up   0.02834   vesicle-associated membrane protein 2 (synaptobrevin 2       32923_r_at   up   0.028392   synapsin I       38515_at   up   0.028404   bone morphogenetic protein 7 (osteogenic protein 1)       32012_at   up   0.02841   pecanex homolog ( Drosophila )       39510_r_at   down   0.028439   programmed cell death 4 (neoplastic transformation                   inhibitor)       34077_at   up   0.028472   chemokine (C—X—C motif) receptor 3       41198_at   up   0.028513   granulin       32649_at   down   0.028531   transcription factor 7 (T-cell specific, HMG-box)       40968_at   up   0.028537   suppressor of cytokine signaling 3       1587_at   up   0.028563   retinoic acid receptor, gamma       38583_at   down   0.028622   UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase,                   polypeptide 2       1859_s_at   up   0.028629   Mdm2, transformed 3T3 cell double minute 2, p53 bindin                   protein (mouse)       36244_at   up   0.028641   zinc finger protein 239       39346_at   down   0.028649   KH domain containing, RNA binding, signal transduction                   associated 1       40607_at   down   0.028666   dihydropyrimidinase-like 2       40659_at   up   0.02869   nuclear receptor subfamily 4, group A, member 3       37112_at   down   0.028745   chromosome 6 open reading frame 32       812_at   down   0.028758   protein phosphatase 1, regulatory (inhibitor) subunit 2       35095_r_at   down   0.028761   leukocyte immunoglobulin-like receptor, subfamily A                   (without TM domain), member 3       35178_at   up   0.028823   WNT inhibitory factor 1       40655_at   up   0.028827   huntingtin-associated protein interacting protein (duo)       38082_at   down   0.02887   KIAA0650 protein       41465_at   down   0.028906   zinc finger protein 148 (pHZ-52)       39932_at   down   0.028952       35417_at   up   0.028976   cubilin (intrinsic factor-cobalamin receptor)       40893_at   down   0.029072   succinate-CoA ligase, ADP-forming, beta subunit       40941_at   up   0.029096   VAMP (vesicle-associated membrane protein)-associate                   protein B and C       40351_at   down   0.029119   guanine nucleotide binding protein (G protein), beta                   polypeptide 3       988_at   down   0.02912   carcinoembryonic antigen-related cell adhesion molecule                   1 (biliary glycoprotein)       34906_g_at   up   0.029139   glutamate receptor, ionotropic, kainate 5       35900_at   up   0.029265   artemin       33138_at   up   0.029266   myeloid leukemia factor 1       36722_s_at   up   0.029339   hepatocyte nuclear factor 4, alpha       38025_r_at   up   0.029343   rap2 interacting protein x       1271_g_at   up   0.029435   v-rel reticuloendotheliosis viral oncogene homolog A,                   nuclear factor of kappa light polypeptide gene enhancer i                   B-cells 3, p65 (avian)       39278_at   up   0.029472   transglutaminase 4 (prostate)       766_at   up   0.029553   lectin, galactoside-binding, soluble, 9 (galectin 9)       36335_at   up   0.029597   butyrophilin, subfamily 1, member A1       38270_at   down   0.02961   poly (ADP-ribose) glycohydrolase       258_at   up   0.029653   lymphotoxin alpha (TNF superfamily, member 1)       38289_r_at   up   0.029684   neurofibromin 1 (neurofibromatosis, von Recklinghausen                   disease, Watson disease)       37336_at   down   0.029708   UBX domain containing 2       35252_at   down   0.02973   KIAA0528 gene product       1102_s_at   down   0.0298   nuclear receptor subfamily 3, group C, member 1                   (glucocorticoid receptor)       38041_at   down   0.029812   UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-                   acetylgalactosaminyltransferase 1 (GalNAc-T1)       36330_at   up   0.029865   cysteine conjugate-beta lyase; cytoplasmic (glutamine                   transaminase K, kyneurenine aminotransferase)       525_g_at   down   0.029867   PMS1 postmeiotic segregation increased 1 ( S. cerevisiae         41458_at   up   0.029904   KIAA0467 protein       32466_at   up   0.029925   ribosomal protein L41       1659_s_at   down   0.029946   Ras homolog enriched in brain 2       35460_at   up   0.029947   G protein-coupled receptor 4       223_at   down   0.02995   ubiquitin-conjugating enzyme E2L 3       34411_at   down   0.030124   3′-phosphoadenosine 5′-phosphosulfate synthase 1       1632_at   up   0.030132       33051_at   up   0.030141   gamma-aminobutyric acid (GABA) receptor, rho 1       1441_s_at   down   0.030183   tumor necrosis factor receptor superfamily, member 6       32946_r_at   up   0.030222   mannose-binding lectin (protein C) 2, soluble (opsonic                   defect)       35258_f_at   down   0.030223   splicing factor, arginine/serine-rich 2, interacting protein       36677_at   down   0.030277   coatomer protein complex, subunit beta 2 (beta prime)       41463_at   up   0.030285   hypothetical protein FLJ38984       36636_at   down   0.030335   ornithine aminotransferase (gyrate atrophy)       39778_at   up   0.030338   mannosyl (alpha-1,3-)-glycoprotein beta-1,2-N-                   acetylglucosaminyltransferase       41000_at   down   0.03037   checkpoint suppressor 1       32065_at   up   0.030391   cAMP responsive element modulator       34372_at   down   0.030409   upstream regulatory element binding protein 1       35424_g_at   up   0.030417   glutamate receptor, metabotropic 5       36835_at   down   0.030439   protein kinase C-like 2       39920_r_at   up   0.030491   C1q-related factor       35408_i_at   down   0.030498   GIOT-2 for gonadotropin inducible transcription repress 2       31878_at   down   0.030618   ATP-binding cassette, sub-family F (GCN20), member 2       38613_at   up   0.03062   putative cyclin G1 interacting protein       41780_at   down   0.03067   protein tyrosine phosphatase, receptor type, f polypeptid                   (PTPRF), interacting protein (liprin), alpha 1       33369_at   down   0.030743   sterol-C4-methyl oxidase-like       34783_s_at   down   0.030757   BUB3 budding uninhibited by benzimidazoles 3 homolog                   (yeast)       35212_at   down   0.03079   ring finger protein 139       38507_at   up   0.030852   cytochrome P450, family 2, subfamily D, polypeptide 6       33163_r_at   down   0.030898   glutamate-cysteine ligase, modifier subunit       36798_g_at   up   0.030948   sialophorin (gpL115, leukosialin, CD43)       39132_at   down   0.031073   SWI/SNF related, matrix associated, actin dependent                   regulator of chromatin, subfamily a, member 5       34534_at   up   0.031122   opioid receptor, mu 1       40074_at   down   0.031215   methylene tetrahydrofolate dehydrogenase (NAD+                   dependent), methenyltetrahydrofolate cyclohydrolase       38293_s_at   up   0.031221   homeo box D3       33237_at   down   0.031222   RNA helicase       36233_at   up   0.031254   3′-phosphoadenosine 5′-phosphosulfate synthase 2       32145_at   up   0.031307   adducin 1 (alpha)       39499_s_at   up   0.031346   par-3 partitioning defective 3 homolog ( C. elegans )       36684_at   down   0.031356   adenosylmethionine decarboxylase 1       34760_at   down   0.031481   C-type lectin BIMLEC precursor       40126_at   up   0.031527   paired mesoderm homeo box 1       31349_at   up   0.031545   DNA-binding protein amplifying expression of surfactant                   protein B       1007_s_at   up   0.031546   discoidin domain receptor family, member 1       37185_at   up   0.031584   serine (or cysteine) proteinase inhibitor, clade B                   (ovalbumin), member 2       32100_r_at   up   0.031585   galactosamine (N-acetyl)-6-sulfate sulfatase (Morquio                   syndrome, mucopolysaccharidosis type IVA)       34381_at   down   0.031631   cytochrome c oxidase subunit VIIc       36285_at   up   0.031708   potassium inwardly-rectifying channel, subfamily J,                   member 4       171_at   down   0.031713   von Hippel-Lindau binding protein 1       39659_at   down   0.031715   Ts translation elongation factor, mitochondrial       37289_at   up   0.031818   cadherin 8, type 2       36218_g_at   up   0.031859   serine/threonine kinase 38       31410_at   up   0.031863   tumor necrosis factor receptor superfamily, member 13B       35387_r_at   up   0.031917   acetylcholinesterase (YT blood group)       33598_r_at   down   0.031933   cold autoinflammatory syndrome 1       38435_at   down   0.031934   peroxiredoxin 4       36510_at   down   0.031942   general transcription factor IIF, polypeptide 2, 30 kDa       41048_at   down   0.031992   phorbol-12-myristate-13-acetate-induced protein 1       38441_s_at   down   0.03202   membrane cofactor protein (CD46, trophoblast-                   lymphocyte cross-reactive antigen)       39483_s_at   down   0.032042   integrin, beta 1 (fibronectin receptor, beta polypeptide,                   antigen CD29 includes MDF2, MSK12)       31889_at   up   0.032073   melan-A       39443_s_at   down   0.032107   cytochrome c oxidase subunit Vb       40172_g_at   up   0.032138   frequently rearranged in advanced T-cell lymphomas 2       36580_at   down   0.032164   hypothetical protein FLJ13910       1140_at   down   0.032164   integrin, alpha E (antigen CD103, human mucosal                   lymphocyte antigen 1; alpha polypeptide)       37877_at   up   0.032166   DKFZP564C103 protein       38402_at   down   0.032188   lysosomal-associated membrane protein 2       39037_at   down   0.032197   myeloid/lymphoid or mixed-lineage leukemia (trithorax                   homolog,  Drosophila ); translocated to, 2       34830_at   up   0.032228   hypothetical protein DKFZp564K0822       32313_at   up   0.032235   tropomyosin 2 (beta)       36332_at   up   0.032309   arylalkylamine N-acetyltransferase       36979_at   up   0.032388   solute carrier family 2 (facilitated glucose transporter),                   member 3       32892_at   up   0.032417   ribosomal protein S6 kinase, 90 kDa, polypeptide 2       1818_at   down   0.032454       38040_at   down   0.032494   splicing factor 30, survival of motor neuron-related       31771_at   up   0.032514       37006_at   down   0.032531   immunoglobulin J polypeptide, linker protein for                   immunoglobulin alpha and mu polypeptides       35310_at   up   0.032585       2090_i_at   up   0.032631       36647_at   down   0.032661   hypothetical protein FLJ10326       35259_s_at   down   0.032688   splicing factor, arginine/serine-rich 2, interacting protein       1105_s_at   up   0.032709   T cell receptor beta locus       31904_at   up   0.03274   phosphodiesterase 2A, cGMP-stimulated       40207_g_at   down   0.032759   chymotrypsin-like       38397_at   down   0.03281   polymerase (DNA-directed), delta 4       38681_at   down   0.03289   eukaryotic translation initiation factor 3, subunit 6 48 kDa       37164_at   up   0.032937   Rhesus blood group, D antigen       37944_at   down   0.032989   GTP cyclohydrolase 1 (dopa-responsive dystonia)       34091_s_at   up   0.033014   vimentin       34008_at   up   0.033133   RAS (RAD and GEM)-like GTP-binding       39879_s_at   up   0.033144   hypothetical protein FLJ10120       37178_at   up   0.03329   hypothetical protein BC017169       36444_s_at   down   0.033356   chemokine (C—C motif) ligand 23       33574_at   up   0.033458   chromosome 6 open reading frame 10       39725_at   down   0.033516   RNA-binding region (RNP1, RRM) containing 2       33871_s_at   up   0.033547   folate receptor 2 (fetal)       891_at   down   0.033587   YY1 transcription factor       37514_s_at   up   0.033701   mannan-binding lectin serine protease 2       32666_at   up   0.033716   chemokine (C—X—C motif) ligand 12 (stromal cell-derived                   factor 1)       32498_at   up   0.033761   glutamate receptor, metabotropic 2       33967_at   up   0.033788   major histocompatibility complex, class II, DO alpha       34280_at   up   0.033821   gamma-aminobutyric acid (GABA) A receptor, epsilon       32178_r_at   down   0.033864   synaptosomal-associated protein, 23 kDa       39701_at   up   0.033899   paternally expressed 3       38715_at   up   0.033904   glycophorin B (includes Ss blood group)       40144_at   down   0.033918   protein tyrosine phosphatase, non-receptor type substr 1       41830_at   down   0.033922   KIAA0494 gene product       35211_at   up   0.034035   protein phosphatase 2 (formerly 2A), regulatory subunit                   B″, alpha       38123_at   down   0.034045   chromosome 10 open reading frame 7       39341_at   up   0.034163   thyroid hormone receptor interactor 6       33651_at   up   0.034184   aquaporin 8       41549_s_at   down   0.034205   adaptor-related protein complex 1, sigma 2 subunit       40897_at   down   0.034209   phosphodiesterase 6A, cGMP-specific, rod, alpha       37586_at   up   0.034298   zinc finger protein 142 (clone pHZ-49)       32175_at   down   0.034333   CDC10 cell division cycle 10 homolog ( S. cerevisiae )       34368_at   down   0.034371   histone deacetylase 2       40859_at   down   0.034403   nuclear protein UKp68       35588_at   down   0.034495   zinc finger protein 443       33977_at   up   0.034609   growth factor independent 1       623_s_at   down   0.034643   RAB2, member RAS oncogene family       41747_s_at   down   0.034656   MADS box transcription enhancer factor 2, polypeptide                   (myocyte enhancer factor 2A)       33381_at   down   0.034676   nuclear receptor coactivator 3       35367_at   down   0.03477   lectin, galactoside-binding, soluble, 3 (galectin 3)       1964_g_at   up   0.034805   fms-related tyrosine kinase 1 (vascular endothelial growt                   factor/vascular permeability factor receptor)       41637_at   up   0.034911   dexamethasone-induced transcript       39888_at   up   0.034927   UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase,                   polypeptide 5       38847_at   up   0.034942   maternal embryonic leucine zipper kinase       36897_at   up   0.034982   megalencephalic leukoencephalopathy with subcortical                   cysts 1       37984_s_at   down   0.035019   ADP-ribosylation factor 6       41505_r_at   down   0.035043   v-maf musculoaponeurotic fibrosarcoma oncogene                   homolog (avian)       1292_at   up   0.035215   dual specificity phosphatase 2       35505_at   up   0.035231   SWI/SNF related, matrix associated, actin dependent                   regulator of chromatin, subfamily f, member 1       38664_at   down   0.035232   craniofacial development protein 1       35572_f_at   down   0.035287   zinc finger protein 253       32281_at   up   0.035303   sorting nexin 15       32478_f_at   down   0.035339       32094_at   up   0.035363   carbohydrate (chondroitin 6) sulfotransferase 3       38597_f_at   up   0.035398   solute carrier family 11 (proton-coupled divalent metal io                   transporters), member 1       41446_f_at   up   0.035415   RNA helicase-related protein       38711_at   down   0.035439   cytoplasmic linker associated protein 2       1017_at   down   0.035486       39288_at   up   0.035547   nectin-like protein 1       710_at   up   0.035599   procollagen-proline, 2-oxoglutarate 4-dioxygenase (proli                   4-hydroxylase), beta polypeptide (protein disulfide                   isomerase; thyroid hormone binding protein p55)       36690_at   down   0.03562   nuclear receptor subfamily 3, group C, member 1                   (glucocorticoid receptor)       33424_at   down   0.035644   ribophorin I       943_at   down   0.035681   runt-related transcription factor 1 (acute myeloid leukem                   1; aml1 oncogene)       39822_s_at   down   0.035691   growth arrest and DNA-damage-inducible, beta       41768_at   down   0.035716   protein kinase, cAMP-dependent, regulatory, type I, alp                   (tissue specific extinguisher 1)       40773_at   up   0.03575   myosin, light polypeptide 5, regulatory       35720_at   down   0.035787   KIAA0893 protein       40151_s_at   down   0.035808   peroxisome receptor 1       1640_at   down   0.035835   suppression of tumorigenicity 13 (colon carcinoma)                   (Hsp70 interacting protein)       41054_at   up   0.035852   KIAA0290 protein       37724_at   down   0.0359   v-myc myelocytomatosis viral oncogene homolog (avian       38654_at   down   0.035915   heterogeneous nuclear ribonucleoprotein U (scaffold                   attachment factor A)       34251_at   up   0.035965   homeo box B5       36974_at   down   0.036018   proteasome (prosome, macropain) inhibitor subunit 1                   (PI31)       34197_at   up   0.036025   phosphoinositide-3-kinase, regulatory subunit, polypepti                   2 (p85 beta)       39092_at   down   0.036029   histone H2A.F/Z variant       38972_at   down   0.036149   hypothetical protein BC013764       34060_g_at   up   0.036265   Pvt1 oncogene homolog, MYC activator (mouse)       32898_at   up   0.036315   actin like protein       40945_at   up   0.03632   TGFB inducible early growth response 2       AFFX-BioDn-   up   0.036336       3_st       37568_at   up   0.036344       37591_at   up   0.036353   uncoupling protein 2 (mitochondrial, proton carrier)       35991_at   down   0.036357   LSM6 homolog, U6 small nuclear RNA associated ( S. cerevisiae )       40193_at   up   0.036372   enolase 2, (gamma, neuronal)       39885_at   down   0.036385   putative dimethyladenosine transferase       239_at   up   0.036478   cathepsin D (lysosomal aspartyl protease)       41279_f_at   up   0.03657   mitogen-activated protein kinase 8 interacting protein 1       32630_f_at   down   0.03659   butyrophilin, subfamily 3, member A1       38985_at   down   0.036653   leptin receptor overlapping transcript-like 1       41510_s_at   down   0.036688   heat shock 70 kDa protein 9B (mortalin-2)       39744_at   down   0.036695   DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3       41561_s_at   down   0.03671   intraflagellar transport protein IFT20       37482_at   up   0.036796   aldo-keto reductase family 1, member B10 (aldose                   reductase)       36968_s_at   down   0.036823   Opa-interacting protein 2       34750_r_at   down   0.036851   zinc finger and BTB domain containing 1       1274_s_at   up   0.036896   cell division cycle 34       35713_at   up   0.036927   Fanconi anemia, complementation group C       37643_at   down   0.036948   tumor necrosis factor receptor superfamily, member 6       34364_at   up   0.036957   peptidylprolyl isomerase E (cyclophilin E)       760_at   down   0.037036   dual-specificity tyrosine-(Y)-phosphorylation regulated                   kinase 2       34965_at   up   0.037053   cystatin F (leukocystatin)       32503_at   down   0.037099   sorting nexin 27       37192_at   up   0.037113   erythrocyte membrane protein band 4.9 (dematin)       39613_at   down   0.037219   mannosidase, alpha, class 1A, member 1       975_at   up   0.03724   serine/threonine kinase 18       37673_at   down   0.037261   neutral sphingomyelinase (N-SMase) activation                   associated factor       34191_at   down   0.037275       1450_g_at   down   0.03728   proteasome (prosome, macropain) subunit, alpha type,       33154_at   down   0.037299   proteasome (prosome, macropain) subunit, beta type, 4       39637_at   down   0.037323   solute carrier family 26 (sulfate transporter), member 2       33781_s_at   up   0.037374   ubiquitin-conjugating enzyme E2M (UBC12 homolog,                   yeast)       38364_at   down   0.037386   transducin-like enhancer of split 4 (E(sp1) homolog,                     Drosophila )       34902_at   up   0.03739   KIAA0492 protein       36516_at   up   0.037461   zinc finger protein ZFP100       949_s_at   down   0.037476   proteasome (prosome, macropain) 26S subunit, ATPas 6       36777_at   up   0.037482   DNA segment on chromosome 12 (unique) 2489                   expressed sequence       38764_at   down   0.037533       1231_at   down   0.037551   ubiquitin-conjugating enzyme E2B (RAD6 homolog)       33765_at   up   0.037599   chemokine (C—X—C motif) ligand 2       34089_at   up   0.037666   KIAA1030 protein       39104_at   up   0.037676       36311_at   up   0.037683   phosphodiesterase 1A, calmodulin-dependent       31636_s_at   up   0.037708   solute carrier family 18 (vesicular acetylcholine), membe 3       32029_at   up   0.037719   3-phosphoinositide dependent protein kinase-1       37107_at   down   0.037821   protein phosphatase ID magnesium-dependent, delta                   isoform       36780_at   up   0.037836   clusterin (complement lysis inhibitor, SP-40, 40, sulfated                   glycoprotein 2, testosterone-repressed prostate messag                   2, apolipoprotein J)       39915_at   up   0.037879   transient receptor potential cation channel, subfamily M,                   member 2       38895_i_at   up   0.038008   neutrophil cytosolic factor 4, 40 kDa       31689_at   down   0.038009   DKFZP564G092 protein       35652_g_at   down   0.038037   mitogen-activated protein kinase kinase kinase 4       37483_at   down   0.038043   histone deacetylase 9       36016_at   up   0.038044   cortistatin       36568_at   up   0.03806   solute carrier family 17 (sodium-dependent inorganic                   phosphate cotransporter), member 7       31411_at   up   0.038106   variable charge, Y chromosome, 2       314_at   down   0.038139   phosphatidylinositol glycan, class B       33761_s_at   up   0.038262   KIAA0493 protein       32983_at   up   0.038292   adrenergic, alpha-1B-, receptor       40143_at   down   0.038345   KIAA0140 gene product       37671_at   down   0.038399   laminin, alpha 4       38727_at   down   0.03847   multiple coagulation factor deficiency protein 2       35535_f_at   up   0.038485   KIAA0565 gene product       35762_at   down   0.038526   KIAA0483 protein       1260_s_at   up   0.038541   glutathione S-transferase A2       35539_at   up   0.038541   interphotoreceptor matrix proteoglycan 1       33067_at   up   0.038554   histone 1, H1a       33450_at   up   0.038556   actin-like 6       34795_at   up   0.038587   procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine                   hydroxylase) 2       35353_at   down   0.038672   proteasome (prosome, macropain) 26S subunit, ATPas 2       390_at   up   0.038847   chemokine (C—C motif) receptor 4       38160_at   down   0.038867   lymphocyte antigen 75       962_at   up   0.038972   BMX non-receptor tyrosine kinase       36347_f_at   up   0.039084   histone 1, H2bn       35221_at   down   0.039152   purine-rich element binding protein A       32043_at   up   0.039176   stanniocalcin 2       1940_at   down   0.039252   v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog       39338_at   down   0.039273   S100 calcium binding protein A10 (annexin II ligand,                   calpactin I, light polypeptide (p11))       40840_at   up   0.039302   peptidylprolyl isomerase F (cyclophilin F)       422_s_at   up   0.03932   MAX protein       32196_at   up   0.039333   TBP-interacting protein       41699_f_at   down   0.039349   bromodomain containing 1       31826_at   up   0.039468   KIAA0674 protein       37309_at   up   0.03947   ras homolog gene family, member A       35262_at   up   0.039475   integrin beta 4 binding protein       2089_s_at   up   0.039507   v-erb-b2 erythroblastic leukemia viral oncogene homolog                   3 (avian)       31798_at   up   0.039562   trefoil factor 1 (breast cancer, estrogen-inducible                   sequence expressed in)       39068_at   up   0.039709   protein phosphatase 2, regulatory subunit B (B56), delta                   isoform       40668_s_at   up   0.039712   CD6 antigen       38405_at   down   0.03972   fragile X mental retardation, autosomal homolog 1       37664_at   up   0.039744   developmentally regulated GTP binding protein 2       39908_at   up   0.039777   TAF6-like RNA polymerase II, p300/CBP-associated                   factor (PCAF)-associated factor, 65 kDa       32209_at   up   0.03978   Mouse Mammary Turmor Virus Receptor homolog 1       37885_at   up   0.039796   hypothetical protein AF038169       38454_g_at   down   0.039796   intercellular adhesion molecule 2       37007_at   down   0.039799   tumor differentially expressed 1       697_f_at   up   0.039946       34643_at   up   0.039976   ribosomal protein S4, X-linked       31331_at   up   0.040002   surfactant protein A binding protein       1726_at   up   0.040012       33208_at   down   0.040098   DnaJ (Hsp40) homolog, subfamily C, member 3       38220_at   down   0.040129   dihydropyrimidine dehydrogenase       36986_at   up   0.040158   lysophospholipase II       41429_at   up   0.040222   protein phosphatase 2 (formerly 2A), regulatory subunit                   (PR 65), beta isoform       34460_at   up   0.040229   benzodiazapine receptor (peripheral) associated protein       762_f_at   up   0.040254   histone 1, H4i       31860_at   down   0.040289   chromosome 17 open reading frame 35       39111_s_at   down   0.040343   peptidylprolyl isomerase (cyclophilin)-like 2       40102_at   down   0.040375   oxysterol binding protein-like 2       35719_at   down   0.040521   pleckstrin homology domain containing, family E (with                   leucine rich repeats) member 1       34605_at   up   0.040586   activating transcription factor 7       37324_at   down   0.040601   transferrin receptor (p90, CD71)       41692_at   down   0.040613   synaptojanin 1       39345_at   down   0.040629   Niemann-Pick disease, type C2       40612_at   down   0.040677   KIAA1117 protein       38690_at   down   0.040763   chromosome 3 open reading frame 4       41046_s_at   up   0.040853   zinc finger protein 261       38450_at   down   0.040905   Sjogren syndrome antigen B (autoantigen La)       31461_at   up   0.041106   proteasome (prosome, macropain) 26S subunit, non-                   ATPase, 4, pseudogene       32087_at   down   0.041149   heat shock transcription factor 2       317_at   up   0.041156   legumain       32204_at   up   0.04122   phosphodiesterase 6G, cGMP-specific, rod, gamma       37242_at   down   0.041221   hypothetical protein MGC5149       35163_at   down   0.041239   KIAA1041 protein       34047_at   up   0.041244   ovo-like 1( Drosophila )       292_s_at   down   0.041287       37889_at   up   0.041327   CD47 antigen (Rh-related antigen, integrin-associated                   signal transducer)       706_at   down   0.04142       1946_at   up   0.041472   Wilms tumor associated protein       34067_at   up   0.041485   type II transmembrane serine protease 6       41698_at   up   0.041503   solute carrier family 9 (sodium/hydrogen exchanger),                   isoform 8       36325_at   up   0.041595   crystallin, beta A1       39103_s_at   up   0.041671       39319_at   down   0.041707   lymphocyte cytosolic protein 2 (SH2 domain containing                   leukocyte protein of 76 kDa)       39621_at   up   0.04171   KIAA0459 protein       32830_g_at   down   0.041825   translocase of inner mitochondrial membrane 17 homolo                   A (yeast)       34816_at   down   0.041866   E1A binding protein p400       32736_at   up   0.041867   ras-related C3 botulinum toxin substrate 2 (rho family,                   small GTP binding protein Rac2)       33553_r_at   down   0.041915   chemokine (C—C motif) receptor 6       1521_at   down   0.041957   non-metastatic cells 1, protein (NM23A) expressed in       35290_at   down   0.041996   hypothetical protein FLJ31657       34430_at   up   0.042007   glutamic-pyruvate transaminase (alanine                   aminotransferase)       34376_at   up   0.042019   protein kinase (cAMP-dependent, catalytic) inhibitor                   gamma       1323_at   down   0.042034   ubiquitin B       1537_at   up   0.042061   epidermal growth factor receptor (erythroblastic leukemia                   viral (v-erb-b) oncogene homolog, avian)       33008_at   up   0.042078   olfactory receptor, family 7, subfamily E, member 24                   pseudogene       32918_at   up   0.0422       39027_at   down   0.042311   cytochrome c oxidase subunit IV isoform 1       41436_at   down   0.042331   zinc finger protein 198       34864_at   up   0.042446   hypothetical protein CGI-57       39503_s_at   up   0.042509   dihydropyrimidinase-like 4       35709_at   down   0.042524   hypothetical protein FLJ11149       37011_at   down   0.04259   allograft inflammatory factor 1       31439_f_at   up   0.042596   Rhesus blood group, CcEe antigens       39557_at   down   0.042673       40019_at   down   0.042779   ecotropic viral integration site 2B       32499_at   up   0.04278   Rho GDP dissociation inhibitor (GDI) gamma       35854_at   down   0.042925   solute carrier family 18 (vesicular monoamine), member 2       34840_at   down   0.042926       37936_at   down   0.043001   PRP4 pre-mRNA processing factor 4 homolog (yeast)       36099_at   down   0.043002   splicing factor, arginine/serine-rich 1 (splicing factor 2,                   alternate splicing factor)       39530_at   up   0.043068   enigma (LIM domain protein)       40926_at   up   0.043095   solute carrier family 6 (neurotransmitter transporter,                   creatine), member 8       AFFX-BioB-3_at   up   0.043174       34135_at   up   0.043181       31544_at   up   0.043193   forkhead box I1       38276_at   down   0.043244   nuclear factor of kappa light polypeptide gene enhancer                   B-cells inhibitor, epsilon       35166_at   down   0.043337   Down syndrome critical region gene 3       41394_at   up   0.043359   phospholipase D2       33339_g_at   down   0.043366   signal transducer and activator of transcription 1, 91 kDa       33317_at   down   0.043374   cyclin-dependent kinase 7 (MO15 homolog, Xenopus                   laevis, cdk-activating kinase)       33920_at   up   0.043398   diaphanous homolog 1 ( Drosophila )       39897_at   down   0.043457   splicing factor YT521-B       39739_at   down   0.043459   nascent-polypeptide-associated complex alpha                   polypeptide       40596_at   up   0.04355   Treacher Collins-Franceschetti syndrome 1       39794_at   down   0.043575   ubiquitin specific protease 8       41153_f_at   down   0.043582   catenin (cadherin-associated protein), alpha 1, 102 kDa       38503_at   up   0.043583   aldehyde dehydrogenase 1 family, member B1       40220_at   down   0.043623   HMBA-inducible       31752_at   up   0.043695   hypothetical protein FLJ23142       36174_at   down   0.043725   MARCKS-like protein       36197_at   down   0.043728   chitinase 3-like 1 (cartilage glycoprotein-39)       1692_s_at   up   0.043818   GDNF family receptor alpha 2       35513_r_at   up   0.043851   Rho family guanine-nucleotide exchange factor       31566_at   up   0.043873       32161_at   down   0.043989   seven in absentia homolog 1 ( Drosophila )       34277_at   up   0.044051   carbonic anhydrase XI       38808_at   up   0.044055   adhesion regulating molecule 1       40864_at   down   0.044105   ras-related C3 botulinum toxin substrate 1 (rho family,                   small GTP binding protein Rac1)       35388_at   up   0.044116   LIM homeobox protein 1       251_at   down   0.04425   calcium/calmodulin-dependent protein kinase I       34792_at   down   0.044292   S-adenosylhomocysteine hydrolase-like 1       32007_at   up   0.044325       39163_at   down   0.04434   likely homolog of rat kinase D-interacting substance of                   220 kDa       31676_at   up   0.044351   zinc finger protein 208       38323_at   down   0.044372   carboxypeptidase, vitellogenic-like       32028_at   up   0.044373   phosphomannomutase 2       34959_at   up   0.044378   Fc fragment of IgE, low affinity II, receptor for (CD23A)       35193_at   down   0.044416   chromosome condensation 1-like       33415_at   down   0.044429   non-metastatic cells 2, protein (NM23B) expressed in       37356_r_at   down   0.044508   vesicle docking protein p115       33950_g_at   up   0.044544   corticotropin releasing hormone receptor 2       36913_at   down   0.044573   stem-loop (histone) binding protein       41559_at   down   0.044597   KIAA1201 protein       38187_at   down   0.04461   N-acetyltransferase 1 (arylamine N-acetyltransferase)       40972_at   down   0.044616   v-akt murine thymoma viral oncogene homolog 2       595_at   down   0.04463   tumor necrosis factor, alpha-induced protein 3       34693_at   down   0.044662   sialyltransferase       34870_at   up   0.044673   LIM domain binding 3       1116_at   up   0.044741   CD19 antigen       36490_s_at   up   0.044883   phosphoribosyl pyrophosphate synthetase 1       37696_at   down   0.044938   voltage-dependent anion channel 2       32369_at   up   0.044951   serum amyloid A4, constitutive       36537_at   down   0.044967   Rho-specific guanine nucleotide exchange factor p114       279_at   down   0.044968   nuclear receptor subfamily 4, group A, member 1       35379_at   up   0.045025   collagen, type IX, alpha 1       1573_at   up   0.045053   platelet-derived growth factor beta polypeptide (simian                   sarcoma viral (v-sis) oncogene homolog)       38247_at   down   0.045143   coagulation factor II (thrombin) receptor-like 1       39763_at   up   0.045196   hemopexin       1093_at   down   0.045205   protein phosphatase 2 (formerly 2A), regulatory subunit                   (PR 65), beta isoform       36238_at   up   0.045459   myeloid/lymphoid or mixed-lineage leukemia (trithorax                   homolog,  Drosophila ); translocated to, 7       31434_at   up   0.045471       36177_at   down   0.04549   translin       39270_at   up   0.045516   CD209 antigen-like       32547_at   down   0.045552   mannose-6-phosphate receptor (cation dependent)       32948_at   up   0.045614   Usher syndrome 2A (autosomal recessive, mild)       39028_at   down   0.045662   karyopherin (importin) beta 3       34634_s_at   up   0.045678   5-hydroxytryptamine (serotonin) receptor 7 (adenylate                   cyclase-coupled)       38544_at   up   0.04577   inhibin, alpha       41597_s_at   down   0.045846   SEC22 vesicle trafficking protein-like 1 ( S. cerevisiae )       38144_at   up   0.045854   hypothetical protein DKFZp667B1218       39758_f_at   up   0.045944   lysosomal-associated membrane protein 1       38436_at   down   0.045972   KIAA0252 protein       32143_at   up   0.045998   odd-skipped-related 2A protein       37391_at   down   0.046076   cathepsin L       41860_at   down   0.046107   hypothetical protein BC015148       1913_at   down   0.046111   cyclin G2       244_at   down   0.046131   heat shock transcription factor 1       38746_at   up   0.046186   integrin, beta 4       35896_at   up   0.046222   DKFZp434P211 protein       40115_at   down   0.046251   ATP synthase, H+ transporting, mitochondrial F1 comple                   gamma polypeptide 1       35251_at   down   0.046264   human immunodeficiency virus type I enhancer binding                   protein 1       1678_g_at   up   0.046272   insulin-like growth factor binding protein 5       32389_at   up   0.046313   RNA, U2 small nuclear       40951_at   up   0.04634   BTG3 associated nuclear protein       33708_at   up   0.046346   prostate cancer overexpressed gene 1       41530_at   down   0.046412   acetyl-Coenzyme A acyltransferase 2 (mitochondrial 3-                   oxoacyl-Coenzyme A thiolase)       40049_at   down   0.046435   death-associated protein kinase 1       37276_at   down   0.04647   IQ motif containing GTPase activating protein 2       37512_at   up   0.046491   3-hydroxysteroid epimerase       33862_at   up   0.046504   phosphatidic acid phosphatase type 2B       1427_g_at   down   0.046519   Src-like-adaptor       34367_at   up   0.04653   phosphoglycerate dehydrogenase       38823_s_at   down   0.0466   serine/threonine kinase 17a (apoptosis-inducing)       1257_s_at   up   0.046621   quiescin Q6       37237_at   up   0.046666   adaptor-related protein complex 3, mu 2 subunit       38747_at   up   0.046695   CD34 antigen       35038_at   up   0.046799   myosin binding protein C, cardiac       39046_at   down   0.046853   histone H2A.F/Z variant       35109_at   up   0.046897   neurofascin       34586_s_at   up   0.046906   distal-less homeo box 2       37522_r_at   down   0.046935   nucleolar cysteine-rich protein       40160_at   down   0.046944   POM121 membrane glycoprotein (rat)       40791_at   up   0.046947   polymerase (RNA) II (DNA directed) polypeptide A,                   220 kDa       31357_at   up   0.046987       33808_at   up   0.046995   TEA domain family member 3       40831_at   down   0.047033   DKFZP586B0923 protein       37938_at   down   0.047074   acidic 82 kDa protein mRNA       35858_at   up   0.047084   postmeiotic segregation increased 2-like 9       33466_at   up   0.047098   hypothetical gene supported by AF038182; BC009203       783_at   down   0.047127   WW domain-containing protein 1       36232_at   up   0.047127   fibroblast growth factor 13       33947_at   up   0.047147   G protein-coupled receptor 3       40317_at   up   0.047216   amiloride-sensitive cation channel 1, neuronal (degener       39782_at   down   0.047224   nuclear DNA-binding protein       35829_at   up   0.04723   immunoglobulin superfamily, member 4       38193_at   up   0.047282   immunoglobulin kappa constant       31510_s_at   down   0.047301   H3 histone, family 3B (H3.3B)       41303_r_at   down   0.047306   hypothetical protein dJ465N24.2.1       37831_at   up   0.047318   KIAA0545 protein       38138_at   up   0.047335   S100 calcium binding protein A11 (calgizzarin)       32852_at   up   0.047348   thioredoxin 2       31408_at   up   0.047356   retinal pigment epithelium-derived rhodopsin homolog       38758_at   up   0.047434   PDGFA associated protein 1       37905_r_at   up   0.047444       41572_r_at   down   0.047457   v-rel reticuloendotheliosis viral oncogene homolog (avian       35294_at   down   0.047527   Sjogren syndrome antigen A2 (60 kDa, ribonucleoprotein                   autoantigen SS-A/Ro)       40494_at   up   0.047561   death effector domain containing       37510_at   down   0.047611   syntaxin 8       39056_at   down   0.047621   phosphoribosylaminoimidazole carboxylase,                   phosphoribosylaminoimidazole succinocarboxamide                   synthetase       38527_at   down   0.047648   non-POU domain containing, octamer-binding       37713_at   up   0.047659   aminoacylase 1       39755_at   up   0.047681   X-box binding protein 1       31816_at   up   0.047754   glucosidase, alpha; acid (Pompe disease, glycogen                   storage disease type II)       31381_at   up   0.048043   peptidoglycan recognition protein       32240_at   up   0.048048   proteasome (prosome, macropain) 26S subunit, non-                   ATPase, 5       40105_at   down   0.048138   methylmalonyl Coenzyme A mutase       35311_at   down   0.048157   cellular repressor of E1A-stimulated genes       39122_at   up   0.048174   glucose phosphate isomerase       37640_at   down   0.048183   hypoxanthine phosphoribosyltransferase 1 (Lesch-Nyhar                   syndrome)       36313_at   down   0.048202   ecotropic viral integration site 2A       32052_at   up   0.048233   hemoglobin, beta       32928_at   up   0.048347   POU domain, class 2, transcription factor 3       40519_at   down   0.048417   protein tyrosine phosphatase, receptor type, C       40910_at   down   0.048437   capping protein (actin filament) muscle Z-line, alpha 1       39139_at   down   0.048449   signal peptidase complex (18 kD)       35184_at   down   0.048653   hypothetical protein MGC23401       38319_at   down   0.048706   CD3D antigen, delta polypeptide (TiT3 complex)       32716_at   up   0.048729   diacylglycerol kinase, alpha 80 kDa       37931_at   up   0.048751   centromere protein B, 80 kDa       41435_at   up   0.048872   protein tyrosine phosphatase, receptor type, f polypeptid                   (PTPRF), interacting protein (liprin), alpha 3       40833_r_at   down   0.048945   lamina-associated polypeptide 1B       34292_at   down   0.048964   chromosome X open reading frame 12       38368_at   down   0.048974   dUTP pyrophosphatase       33395_at   up   0.048977   DKFZP566C0424 protein       36432_at   up   0.049021   methylcrotonoyl-Coenzyme A carboxylase 2 (beta)       36920_at   down   0.049082   myotubular myopathy 1       35830_at   up   0.049138   exportin 6       39531_at   up   0.049147   microtubule-associated protein 1B       31710_at   up   0.049156       35550_at   down   0.04917   phosphate cytidylyltransferase 1, choline, beta isoform       32643_at   up   0.049176   glucan (1,4-alpha-), branching enzyme 1 (glycogen                   branching enzyme, Andersen disease, glycogen storage                   disease type IV)       1213_at   down   0.049284   SFRS protein kinase 2       38765_at   down   0.049409   Dicer1, Dcr-1 homolog ( Drosophila )       777_at   down   0.049529   GDP dissociation inhibitor 2       39854_r_at   up   0.049529   transport-secretion protein 2.2       36118_at   down   0.049576   nuclear receptor coactivator 1       39009_at   down   0.049585   LSM3 homolog, U6 small nuclear RNA associated ( S. cerevisiae )       40106_at   up   0.049587   E1B-55 kDa-associated protein 5       32597_at   down   0.049613   retinoblastoma-like 2 (p130)       37423_at   up   0.049689   solute carrier family 12 (sodium/potassium/chloride                   transporters), member 2       32792_at   down   0.049898   GCIP-interacting protein p29       37900_at   down   0.049937   peroxisomal biogenesis factor 11B       218_at   down   0.050114   IK cytokine, down-regulator of HLA II       1983_at   up   0.050135   cyclin D2       38199_at   up   0.050157   similar to RIKEN cDNA 2610307I21       35370_at   down   0.050158   SPTF-associated factor 65 gamma       36509_at   down   0.050193   ribosomal protein L35a       41855_at   down   0.050238   histone acetyltransferase 1       33921_at   up   0.050257   glucose-6-phosphatase, transport (glucose-6-phosphate)                   protein 1       32338_at   up   0.050322   DKFZP564C152 protein       31573_at   down   0.050336   ribosomal protein S25       35686_s_at   up   0.05038   mature T-cell proliferation 1       34508_r_at   up   0.050407   kinase phosphatase inhibitor 2       39264_at   up   0.050425   2′-5′-oligoadenylate synthetase 2, 69/71 kDa       937_at   down   0.050456       39507_at   down   0.050466   O-linked N-acetylglucosamine (GlcNAc) transferase                   (UDP-N-acetylglucosamine:polypeptide-N-                   acetylglucosaminyl transferase)       36460_at   down   0.05048   polymerase (RNA) I polypeptide C, 30 kDa       1449_at   down   0.050486   proteasome (prosome, macropain) subunit, alpha type, 4       32982_at   down   0.050635   myelin transcription factor 2       41400_at   down   0.050664   thymidine kinase 1, soluble       41266_at   down   0.050685   integrin, alpha 6       336_at   up   0.050688   thromboxane A2 receptor       35083_at   up   0.050695   ferritin, light polypeptide       34563_at   up   0.050709   kinesin family member 14       39951_at   up   0.050726   plastin 1 (I isoform)       469_at   up   0.05075   ephrin-B3       1589_s_at   down   0.050778   interferon (alpha, beta and omega) receptor 2       32915_at   up   0.050787       32319_at   up   0.050795   tumor necrosis factor (ligand) superfamily, member 4 (ta                   transcriptionally activated glycoprotein 1, 34 kDa)       40516_at   down   0.050823   aryl hydrocarbon receptor       40762_g_at   down   0.050837   solute carrier family 16 (monocarboxylic acid                   transporters), member 5       32872_at   up   0.050892       32598_at   down   0.050917   NEL-like 2 (chicken)       40066_at   down   0.050921   ubiquitin-activating enzyme E1C (UBA3 homolog, yeast)       37191_at   up   0.050937   phytanoyl-CoA hydroxylase interacting protein       36731_g_at   up   0.050945   ATP-binding cassette, sub-family C (CFTR/MRP),                   member 10       38032_at   up   0.050977   synaptic vesicle glycoprotein 2A       39891_at   down   0.051005       40727_at   down   0.051151   anaphase-promoting complex subunit 10       34573_at   up   0.051166   ephrin-A3       37575_at   down   0.051171       41837_at   up   0.051172   chromosome 14 open reading frame 132       39706_at   down   0.051192   copine III       39796_at   up   0.051208   proteasome (prosome, macropain) activator subunit 3                   (PA28 gamma; Ki)       37205_at   up   0.051225   F-box and leucine-rich repeat protein 7       33517_f_at   up   0.051227   melanoma antigen, family A, 3       37089_at   up   0.051376   a disintegrin and metalloproteinase domain 3a (cyritestir                   1)       41525_at   up   0.051469   high-mobility group 20B       37387_r_at   down   0.05148   KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein                   retention receptor 1       41753_at   up   0.051513   actinin, alpha 4       40561_at   up   0.05152   T-cell leukemia, homeobox 2       33523_at   up   0.051666   alkaline phosphatase, intestinal       36041_at   up   0.051715   exonuclease 1       39789_at   up   0.051771   sarcolipin       36799_at   up   0.051797   frizzled homolog 2 ( Drosophila )       41493_at   down   0.051813   ATPase, Class VI, type 11A       34820_at   up   0.051886   pleiotrophin (heparin binding growth factor 8, neurite                   growth-promoting factor 1)       36484_at   down   0.051889   UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-                   acetylgalactosaminyltransferase 3 (GalNAc-T3)       40381_at   up   0.051999   KIAA0972 protein       38230_at   up   0.052097   endothelial PAS domain protein 1       33961_at   up   0.052099       40371_at   up   0.052175   dopamine receptor D2       36494_at   down   0.052182   spondyloepiphyseal dysplasia, late, pseudogene       33198_at   down   0.052191   binder of Arl Two       35743_at   up   0.052209   cleavage and polyadenylation specific factor 4, 30 kDa       34791_at   down   0.052211   t-complex 1       32811_at   up   0.05223   myosin IC       37381_g_at   down   0.052289   general transcription factor IIB       379_at   down   0.052302   ATP binding protein associated with cell differentiation       39519_at   down   0.052312   KIAA0692 protein       34167_s_at   up   0.052385   solute carrier family 6 (neurotransmitter transporter, L-                   proline), member 7       31367_at   up   0.052421   KIAA0998 protein       36971_at   down   0.052422   likely ortholog of mouse Rw1       37021_at   down   0.052436   cathepsin H       37620_at   down   0.052482   TAF12 RNA polymerase II, TATA box binding protein                   (TBP)-associated factor, 20 kDa       765_s_at   up   0.052582   lectin, galactoside-binding, soluble, 4 (galectin 4)       39003_at   down   0.052675   pituitary tumor-transforming 1 interacting protein       31962_at   up   0.052686   ribosomal protein L37a       551_at   down   0.052715   E1A binding protein p300       40491_at   up   0.052889   retinoblastoma binding protein 1-like 1       39692_at   down   0.052957   hypothetical protein DKFZp586F2423       32533_s_at   down   0.053017   vesicle-associated membrane protein 5 (myobrevin)       39064_at   down   0.053053   5,10-methenyltetrahydrofolate synthetase (5-                   formyltetrahydrofolate cyclo-ligase)       35957_at   up   0.053064   stannin       36440_at   up   0.053117   pre T-cell antigen receptor alpha       39707_at   down   0.053118   myotubularin related protein 4       32335_r_at   down   0.053145   ubiquitin C       867_s_at   up   0.053202   thrombospondin 1       33545_at   up   0.053202   sodium channel, voltage-gated, type IV, alpha       716_at   up   0.053248   gamma-glutamyltransferase-like activity 1       37490_at   up   0.053251   solute carrier family 4, anion exchanger, member 3       34963_at   up   0.053255   collagen, type XIV, alpha 1 (undulin)       1878_g_at   down   0.053278   excision repair cross-complementing rodent repair                   deficiency, complementation group 1 (includes                   overlapping antisense sequence)       41218_at   down   0.053298   KIAA0570 gene product       37306_at   down   0.053313   cytoplasmic FMR1 interacting protein 1       32654_g_at   down   0.053395   bromodomain containing 8       1180_g_at   down   0.053406       738_at   down   0.053443   5′-nucleotidase, cytosolic II       32843_s_at   up   0.05356   casein kinase 2, beta polypeptide       39818_at   down   0.053596   putative c-Myc-responsive       1984_s_at   up   0.05365   Rho GDP dissociation inhibitor (GDI) beta       34705_at   up   0.053743   similar to yeast BET3 ( S. cerevisiae )       35147_at   up   0.053798   MCF.2 cell line derived transforming sequence-like       36237_at   up   0.053829   solute carrier family 22 (organic anion transporter),                   member 6       39070_at   down   0.053862   fascin homolog 1, actin-bundling protein                   (Strongylocentrotus purpuratus)       39061_at   up   0.053904   bone marrow stromal cell antigen 2       39457_r_at   up   0.053929   sorting nexin 4       40466_at   up   0.053949   nuclear transcription factor Y, gamma       38485_at   down   0.054018   NADH dehydrogenase (ubiquinone) 1, subcomplex                   unknown, 1, 6 kDa       37307_at   up   0.054022   guanine nucleotide binding protein (G protein), alpha                   inhibiting activity polypeptide 2       633_s_at   up   0.054102   transcription factor Dp-2 (E2F dimerization partner 2)       883_s_at   up   0.054292   pim-1 oncogene       815_at   up   0.054384   docking protein 1, 62 kDa (downstream of tyrosine kinase                   1)       39549_at   down   0.054465   neuronal PAS domain protein 2       35748_at   down   0.054501   eukaryotic translation elongation factor 1 beta 2       32488_at   up   0.054503   collagen, type III, alpha 1 (Ehlers-Danlos syndrome type                   IV, autosomal dominant)       1125_s_at   up   0.054566   CD44 antigen (homing function and Indian blood group                   system)       38931_at   down   0.054596   zinc finger protein, X-linked       35047_at   up   0.054596   regulatory factor X, 2 (influences HLA class II expression       36807_at   up   0.054671   TED protein       32745_at   down   0.054805   mitochondrial ribosomal protein L40       33079_at   down   0.054837   syntaxin 6       38195_at   up   0.054849   KIAA0783 gene product       40348_s_at   up   0.054929   acidic (leucine-rich) nuclear phosphoprotein 32 family,                   member E       35675_at   up   0.055021   vinexin beta (SH3-containing adaptor molecule-1)       41655_at   up   0.055041   midline 2       35502_at   up   0.055045   anti-Mullerian hormone receptor, type II       39590_at   up   0.055058   amyloid beta (A4) precursor protein-binding, family A,                   member 2 (X11-like)       39921_at   down   0.05506   cytochrome c oxidase subunit Vb       1904_at   down   0.055112   c-myc binding protein       40326_at   up   0.055127   cerebellin 1 precursor       39364_s_at   up   0.055204   protein phosphatase 1, regulatory (inhibitor) subunit 3C       32860_g_at   down   0.055251   signal transducer and activator of transcription 1, 91 kDa       39899_at   up   0.055292   TSLC1-like 2       38850_at   up   0.055469       37725_at   down   0.055509   protein phosphatase 1, catalytic subunit, gamma isoform       32106_at   up   0.055553   serine (or cysteine) proteinase inhibitor, clade A (alpha-1                   antiproteinase, antitrypsin), member 4       409_at   down   0.055578   tyrosine 3-monooxygenase/tryptophan 5-monooxygenas                   activation protein, theta polypeptide       33715_r_at   down   0.055635   general transcription factor IIH, polypeptide 2, 44 kDa       32587_at   down   0.055636   zinc finger protein 36, C3H type-like 2       38172_at   down   0.055664   carbonyl reductase 3       37436_at   up   0.055701   mitochondrial capsule selenoprotein       41070_r_at   down   0.055707   transcription termination factor, mitochondrial       39841_at   down   0.055715   solute carrier family 16 (monocarboxylic acid                   transporters), member 6       35354_at   up   0.055782   synaptogyrin 1       38526_at   up   0.055797   phosphodiesterase 4D, cAMP-specific                   (phosphodiesterase E3 dunce homolog,  Drosophila )       1412_g_at   up   0.055798   cytochrome P450, family 11, subfamily B, polypeptide 1       37840_at   up   0.055809   cyclic nucleotide gated channel alpha 1       36606_at   up   0.05594   carboxypeptidase E       36163_at   down   0.055944   dihydrolipoamide dehydrogenase (E3 component of                   pyruvate dehydrogenase complex, 2-oxo-glutarate                   complex, branched chain keto acid dehydrogenase                   complex)       34843_at   down   0.056006   KIAA0222 gene product       41418_at   up   0.056134   latrophilin 1       38416_at   down   0.056171   chaperonin containing TCP1, subunit 6A (zeta 1)       36998_s_at   down   0.056286   spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2,                   autosomal dominant, ataxin 2)       34587_at   up   0.0563   eosinophil peroxidase       38627_at   up   0.056394   hepatic leukemia factor       1076_at   down   0.056444   interleukin 1, alpha       1337_s_at   up   0.056459   retinoic acid receptor, alpha       AFFX-BioDn-   up   0.056496       5_at       37694_at   down   0.056501   PHD finger protein 3       39337_at   down   0.056519   H2A histone family, member Z       37077_at   up   0.056579   pyruvate kinase, liver and RBC       38371_at   down   0.056601   proteasome (prosome, macropain) subunit, alpha type, 1       33205_at   up   0.056644   suppressor of Ty 3 homolog ( S. cerevisiae )       33281_at   up   0.056699   inhibitor of kappa light polypeptide gene enhancer in B-                   cells, kinase epsilon       32303_at   up   0.05673   ets variant gene 3       32546_at   down   0.056793   fumarate hydratase       734_at   up   0.0568       35022_at   up   0.056829   SRY (sex determining region Y)-box 5       32224_at   down   0.056859   KIAA0769 gene product       37001_at   down   0.056907   calpain 2, (m/II) large subunit       39991_at   up   0.056999   corneodesmosin       41496_at   up   0.057011   HCF-binding transcription factor Zhangfei       39894_f_at   down   0.057027   bromodomain containing 1       35824_at   down   0.057055   zinc finger protein 238       37499_at   up   0.057095   KIAA0408 gene product       36446_s_at   down   0.057135   hepatoma-derived growth factor (high-mobility group                   protein 1-like)       37994_at   down   0.057304   fragile X mental retardation 1       33670_at   up   0.057341       41622_r_at   down   0.05735   zinc finger protein 266       41294_at   up   0.057454   keratin 7       39747_at   down   0.057465   polymerase (RNA) II (DNA directed) polypeptide G       2068_s_at   down   0.057538   E2F transcription factor 2       37751_at   down   0.057572   KIAA0255 gene product       33039_at   down   0.057696   T-cell receptor interacting molecule       1621_at   down   0.057779   CDC5 cell division cycle 5-like ( S. pombe )       182_at   up   0.057817   inositol 1,4,5-triphosphate receptor, type 3       31587_at   up   0.057841   solute carrier family 14 (urea transporter), member 2       34402_at   down   0.057844   unr-interacting protein       36620_at   down   0.057858   superoxide dismutase 1, soluble (amyotrophic lateral                   sclerosis 1 (adult))       39439_at   up   0.057864       40738_at   up   0.057874   CD2 antigen (p50), sheep red blood cell receptor       36165_at   down   0.057904   cytochrome c oxidase subunit VIc       35267_g_at   down   0.057925   bladder cancer associated protein       41858_at   up   0.057932   FGF receptor activating protein 1       32013_at   down   0.057996   zinc finger protein 409       35958_at   up   0.058051   ADP-ribosylation factor-like 7       31851_at   down   0.058101   ret finger protein 2       33069_f_at   up   0.058119   UDP glycosyltransferase 2 family, polypeptide B15       32392_s_at   up   0.058127   UDP glycosyltransferase 1 family, polypeptide A4       39150_at   down   0.058159   ring finger protein 11       35831_at   up   0.058337   ATPase, Class II, type 9A       35434_at   up   0.058387   MADS box transcription enhancer factor 2, polypeptide D                   (myocyte enhancer factor 2D)       39412_at   up   0.058422   tripartite motif-containing 26       39294_at   up   0.058457   nuclear receptor subfamily 2, group F, member 1       41638_at   down   0.058458   KIAA0073 protein       34404_at   down   0.05849   COP9 constitutive photomorphogenic homolog subunit 7                   ( Arabidopsis )       32733_at   down   0.05852   mitochondrial ribosomal protein S14       33706_at   up   0.058622   squamous cell carcinoma antigen recognised by T cells       40578_s_at   up   0.058655   tropomodulin 1       37165_f_at   up   0.058858   Rhesus blood group, CcEe antigens       35172_at   down   0.058889   tyrosylprotein sulfotransferase 2       AFFX-DapX-3_at   up   0.05895       41705_at   up   0.059029   radical fringe homolog ( Drosophila )       1735_g_at   up   0.059035   transforming growth factor, beta 3       36687_at   down   0.059039   cytochrome c oxidase subunit VIIb       33403_at   down   0.059201   DKFZP547E1010 protein       553_g_at   down   0.059352   Rho GTPase activating protein 1       31869_at   down   0.059449   SWAP-70 protein       715_s_at   up   0.059541   gamma-glutamyltransferase 1       40688_at   up   0.059541   linker for activation of T cells       33514_at   down   0.059565   calcium/calmodulin-dependent protein kinase IV       38019_at   up   0.059588   casein kinase 1, epsilon       36570_at   up   0.059666   calbindin 1, 28 kDa       1680_at   up   0.059714   growth factor receptor-bound protein 7       2015_s_at   down   0.059737   PMS2 postmeiotic segregation increased 2 ( S. cerevisiae         331_at   up   0.059749       32117_at   up   0.059788   apoptosis antagonizing transcription factor       32606_at   down   0.059843   brain abundant, membrane attached signal protein 1       38256_s_at   down   0.059857   DKFZP564O092 protein       1657_at   up   0.059889   protein tyrosine phosphatase, receptor type, R       38414_at   down   0.060003   CDC20 cell division cycle 20 homolog ( S. cerevisiae )       40710_at   up   0.060006   calmegin       36506_at   down   0.060098   A kinase (PRKA) anchor protein (yotiao) 9       36517_at   down   0.060144   U2(RNU2) small nuclear RNA auxillary factor 1       38314_at   up   0.060166   capicua homolog ( Drosophila )       38031_at   down   0.06017   KIAA0111 gene product       1915_s_at   up   0.060242   v-fos FBJ murine osteosarcoma viral oncogene homolog       1250_at   down   0.060379   protein kinase, DNA-activated, catalytic polypeptide       31309_r_at   up   0.060453       31318_at   up   0.060492       38183_at   down   0.060518   forkhead box F1       35953_at   up   0.060518   carboxypeptidase N, polypeptide 1, 50 kD       40482_s_at   up   0.060522   transcriptional activator of the c-fos promoter       34073_s_at   up   0.060534   guanine nucleotide binding protein (G protein), alpha                   transducing activity polypeptide 1       499_at   up   0.060624   MAD1 mitotic arrest deficient-like 1 (yeast)       34096_at   up   0.060635   KIAA0912 protein       40453_s_at   down   0.060669   splicing factor, arginine/serine-rich 5       35554_f_at   up   0.060751   Zic family member 2 (odd-paired homolog,  Drosophila )       38281_at   down   0.060874   caspase 7, apoptosis-related cysteine protease       41807_at   down   0.060901   sin3-associated polypeptide, 18 kDa       35374_at   up   0.060921   rootletin       41506_at   down   0.060926   mitogen-activated protein kinase-activated protein kinase 5       32194_at   down   0.06103   CCAAT-box-binding transcription factor       386_g_at   up   0.0611       36572_r_at   down   0.06115   ADP-ribosylation factor-like 6 interacting protein       32965_f_at   up   0.061162   heat shock 70 kDa protein 1B       34814_at   down   0.06127   SUMO-1 activating enzyme subunit 2       39399_at   up   0.061337   tubulin-specific chaperone d       38872_at   up   0.061352   zinc finger protein 230       31539_r_at   up   0.061358       38483_at   up   0.061407   dullard homolog ( Xenopus laevis )       838_s_at   up   0.061516   ubiquitin-conjugating enzyme E2I (UBC9 homolog, yeast       41833_at   up   0.061566   jumping translocation breakpoint       33004_g_at   up   0.06165   NCK adaptor protein 2       39151_at   up   0.061669   astrotactin       33952_at   up   0.06176   zinc finger protein 306       35575_f_at   up   0.061928   zinc finger protein 253       40567_at   down   0.061963   tubulin, alpha 3       905_at   down   0.061983   guanylate kinase 1       39133_at   down   0.061983   GCN5 general control of amino-acid synthesis 5-like 1                   (yeast)       41669_at   down   0.062016   KIAA0191 protein       39048_at   up   0.06202   Notch homolog 4 ( Drosophila )       40134_at   down   0.062031   ATP synthase, H+ transporting, mitochondrial F0 comple                   subunit f, isoform 2       610_at   down   0.062036   adrenergic, beta-2-, receptor, surface       445_at   up   0.062045   NK3 transcription factor related, locus 1 ( Drosophila )       36353_at   up   0.062046   hairy and enhancer of split ( Drosophila ) homolog 2       40180_at   up   0.062046   insulin receptor substrate 2       32963_s_at   down   0.062118   Rag D protein       1458_at   up   0.062196   protein tyrosine phosphatase, non-receptor type 3       40667_at   up   0.062229   CD6 antigen       34821_at   down   0.062272   chromosome 6 open reading frame 80       38114_at   down   0.062321   RAD21 homolog ( S. pombe )       40409_at   down   0.06235   aldehyde dehydrogenase 3 family, member A2       36900_at   up   0.062386   stromal interaction molecule 1       40604_at   down   0.062441   dual-specificity tyrosine-(Y)-phosphorylation regulated                   kinase 2       37608_g_at   up   0.062657   ketohexokinase (fructokinase)       38607_at   up   0.062688   transmembrane 4 superfamily member 5       31496_g_at   up   0.062707   chemokine (C motif) ligand 2       39005_s_at   down   0.062761   zinc finger protein 294       41038_at   down   0.062773   neutrophil cytosolic factor 2 (65 kDa, chronic                   granulomatous disease, autosomal 2)       731_f_at   up   0.062914       776_at   down   0.062923   phosphatidylinositol glycan, class F       2050_s_at   down   0.06298   ras-related C3 botulinum toxin substrate 1 (rho family,                   small GTP binding protein Rac1)       37892_at   up   0.062998   collagen, type XI, alpha 1       34237_at   down   0.063043   HBS1-like ( S. cerevisiae )       AFFX-   up   0.063076   glyceraldehyde-3-phosphate dehydrogenase       HUMGAPDH/M3       3197_M_at       41023_at   up   0.063109   complement component 8, alpha polypeptide       38408_at   up   0.063134   transmembrane 4 superfamily member 2       35552_at   up   0.063161   phosphate cytidylyltransferase 1, choline, beta isoform       36058_at   up   0.063188   ASC-1 complex subunit P100       32592_at   up   0.063295   KIAA0323 protein       32559_s_at   down   0.063304   LSM4 homolog, U6 small nuclear RNA associated ( S. cerevisiae )       31675_s_at   down   0.063337   phosphatase and tensin homolog (mutated in multiple                   advanced cancers 1), pseudogene 1       34003_at   down   0.06334   triosephosphate isomerase 1       34412_s_at   up   0.06344   peanut-like 1 ( Drosophila )       37853_at   up   0.063455   urocortin       40125_at   down   0.063554   calnexin       36148_at   up   0.063582   amyloid beta (A4) precursor-like protein 1       35078_at   up   0.063583   intercellular adhesion molecule 4, Landsteiner-Wiener                   blood group       32967_at   up   0.06359   regulator of Fas-induced apoptosis       35939_s_at   up   0.063597   POU domain, class 4, transcription factor 1       40777_at   down   0.063706   catenin (cadherin-associated protein), beta 1, 88 kDa       33448_at   up   0.063706   serine protease inhibitor, Kunitz type 1       36845_at   down   0.063755   nuclear matrix protein NXP2       33678_i_at   up   0.063774   tubulin, beta, 2       1956_s_at   up   0.063778       34993_at   up   0.063791   sarcoglycan, delta (35 kDa dystrophin-associated                   glycoprotein)       39017_at   down   0.063812   LSM1 homolog, U6 small nuclear RNA associated ( S. cerevisiae )       199_s_at   down   0.063818   protein kinase C-like 2       37779_at   up   0.063874   acid sphingomyelinase-like phosphodiesterase       522_s_at   up   0.063911   folate receptor 3 (gamma)       33822_at   up   0.063948   nuclear mitotic apparatus protein 1       34019_at   up   0.063949   cholinergic receptor, nicotinic, alpha polypeptide 3       1453_at   down   0.064036   MAD, mothers against decapentaplegic homolog 2                   ( Drosophila )       31733_at   up   0.064146   purinergic receptor P2X, ligand-gated ion channel, 3       38306_at   down   0.06416   brefeldin A-inhibited guanine nucleotide-exchange protein 1       36276_at   up   0.06418   contactin 2 (axonal)       851_s_at   up   0.064186   insulin receptor substrate 1       556_s_at   up   0.064191   glutathione S-transferase M4       35661_g_at   up   0.064238   S-antigen; retina and pineal gland (arrestin)       39339_at   up   0.064293   KIAA0792 gene product       36916_at   up   0.064357   sialyltransferase 4C (beta-galactoside alpha-2,3-                   sialyltransferase)       31559_at   up   0.064387   solute carrier family 13 (sodium-dependent dicarboxylate                   transporter), member 2       35610_at   up   0.06442   matrilin 1, cartilage matrix protein       41145_at   down   0.064477   family with sequence similarity 13, member A1       41681_at   down   0.064546   ATP-binding cassette, sub-family B (MDR/TAP), member 7       32954_at   up   0.064582   DKFZP434D193 protein       32571_at   up   0.064689   methionine adenosyltransferase II, alpha       33684_at   up   0.064701   wingless-type MMTV integration site family, member 2B       38164_at   down   0.064739   retinitis pigmentosa GTPase regulator       32681_at   up   0.064752   solute carrier family 9 (sodium/hydrogen exchanger),                   isoform 1 (antiporter, Na+/H+, amiloride sensitive)       40623_at   down   0.064767   ubiquitin protein ligase       36763_at   up   0.064769   wingless-type MMTV integration site family, member 7A       40838_at   down   0.064777   zinc finger protein 292       40419_at   up   0.064956   stomatin       39195_s_at   up   0.064983   leucine-rich repeats and immunoglobulin-like domains 1       40506_s_at   down   0.065005   poly(A) binding protein, cytoplasmic 4 (inducible form)       38186_g_at   up   0.065027   paired box gene 2       32697_at   down   0.065062   inositol(myo)-1(or 4)-monophosphatase 1       35813_at   up   0.065103   transportin-SR       33895_at   down   0.065122   likely ortholog of mouse Sh3 domain YSC-like 1       40406_at   up   0.065199   macrophage stimulating, pseudogene 9       41162_at   up   0.065234   protein phosphatase 1G (formerly 2C), magnesium-                   dependent, gamma isoform       35368_at   down   0.06526   zinc finger protein 207       35019_at   up   0.065337   zinc finger protein 254       39460_g_at   up   0.065365   ribosomal protein S13       39647_s_at   up   0.065434   calcium channel, voltage-dependent, beta 2 subunit       31801_at   up   0.065498       37081_at   up   0.065507   dynein, axonemal, heavy polypeptide 7       31765_at   up   0.065614   hypothetical protein FLJ20220       38668_at   down   0.065811   KIAA0553 protein       32050_r_at   down   0.065884       35116_at   down   0.065906   KIAA0874 protein       36808_at   up   0.065972   protein tyrosine phosphatase, non-receptor type 22                   (lymphoid)       40854_at   down   0.066118   ubiquinol-cytochrome c reductase core protein II       35673_at   up   0.066212   Rho guanine nucleotide exchange factor (GEF) 5       40269_at   down   0.066219   PRP18 pre-mRNA processing factor 18 homolog (yeast)       1403_s_at   up   0.066241   chemokine (C—C motif) ligand 5       31436_s_at   up   0.066263   estrogen receptor 2 (ER beta)       308_f_at   up   0.066282   growth hormone 2       41476_at   up   0.066339   guanine nucleotide binding protein (G protein), alpha 11                   (Gq class)       1195_s_at   down   0.066371   integrin cytoplasmic domain-associated protein 1       39096_at   down   0.066452   SON DNA binding protein       36945_at   up   0.066499   chromosome 12 open reading frame 8       39036_g_at   down   0.066538   progestin induced protein       41029_at   up   0.066712   U1-snRNP binding protein homolog       35721_at   down   0.0668   hydroxy-delta-5-steroid dehydrogenase, 3 beta- and                   steroid delta-isomerase 1       38949_at   up   0.066925   protein kinase C, theta       38945_at   up   0.067053   metal-regulatory transcription factor 1       34626_at   up   0.06707   hypermethylated in cancer 1       744_at   down   0.067118   DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 8 (RNA                   helicase)       34596_at   up   0.067122   casein kappa       36935_at   down   0.067265   RAS p21 protein activator (GTPase activating protein) 1       1952_s_at   down   0.067351   MAD, mothers against decapentaplegic homolog 5                   ( Drosophila )       41278_at   down   0.067459   BAF53       643_at   up   0.067476   nuclear receptor subfamily 0, group B, member 2       1399_at   down   0.067506   transcription elongation factor B (SIII), polypeptide 1                   (15 kDa, elongin C)       32545_r_at   up   0.067532   Ras suppressor protein 1       34649_at   down   0.067605   decorin       37966_at   up   0.06761   parvin, beta       40832_s_at   down   0.067654   lamina-associated polypeptide 1B       38672_at   up   0.067756   protein phosphatase 1, regulatory subunit 10       35576_f_at   up   0.067819   histone 1, H2bl       33438_at   up   0.067968   WW domain binding protein 2       35481_at   up   0.068025   myosin heavy chain Myr 8       32217_at   down   0.068042   chromosome 12 open reading frame 22       228_at   down   0.068127   v-ral simian leukemia viral oncogene homolog B (ras                   related; GTP binding protein)       464_s_at   down   0.06822   interferon-induced protein 35       39552_at   down   0.068223   phosphatase and tensin homolog (mutated in multiple                   advanced cancers 1)       41110_at   down   0.068425   cullin 5       37023_at   down   0.068458   lymphocyte cytosolic protein 1 (L-plastin)       36948_at   down   0.068499   CREBBP/EP300 inhibitory protein 1       40963_at   up   0.068522   ATP-binding cassette, sub-family A (ABC1), member 4       38633_at   down   0.068526   metastasis associated 1       31339_at   up   0.068694   protease inhibitor 15       AFFX-CreX-5_st   up   0.068736       41051_at   down   0.068762   translin-associated factor X       33842_at   up   0.06881   hypothetical protein FLJ11560       36597_at   down   0.068981   nucleolar and coiled-body phosphoprotein 1       31523_f_at   up   0.068994   histone 1, H2be       41460_at   down   0.069064   RNA binding motif protein 14       36958_at   up   0.069077   zyxin       36483_at   down   0.069179   UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-                   acetylgalactosaminyltransferase 3 (GalNAc-T3)       32274_r_at   up   0.069303       36616_at   down   0.069311   DAZ associated protein 2       39721_at   up   0.069372   ephrin-B1       950_at   down   0.06943   translocation protein 1       33354_at   down   0.069464   E3 ubiquitin ligase SMURF2       40571_at   down   0.0695   myosin VA (heavy polypeptide 12, myoxin)       41343_at   down   0.06951   CDP-diacylglycerol synthase (phosphatidate                   cytidylyltransferase) 2       38159_at   up   0.069545       33989_f_at   up   0.069619   testis enhanced gene transcript (BAX inhibitor 1)       39646_at   up   0.06966   calcium channel, voltage-dependent, beta 2 subunit       39141_at   up   0.069763   ATP-binding cassette, sub-family F (GCN20), member 1       966_at   up   0.069776   RAD54-like ( S. cerevisiae )       40660_at   up   0.069809   nuclear receptor subfamily 4, group A, member 3       35037_at   up   0.069895   solute carrier family 28 (sodium-coupled nucleoside                   transporter), member 1       36978_at   down   0.069901   proteasome (prosome, macropain) activator subunit 4       1446_at   down   0.069924   proteasome (prosome, macropain) subunit, alpha type, 2       41296_s_at   down   0.069939   START domain containing 7       36104_at   down   0.06998   ubiquinol-cytochrome c reductase hinge protein       238_at   down   0.07003   ribosomal protein S6 kinase, 70 kDa, polypeptide 1       36667_at   up   0.070033   phosphorylase, glycogen; brain       39992_at   up   0.070076   solute carrier family 22 (organic cation transporter),                   member 1-like       35864_at   up   0.070114   acrosin       39295_s_at   up   0.070249   Arg/Abl-interacting protein ArgBP2       38522_s_at   down   0.070415   CD22 antigen       40916_at   down   0.070458   hypothetical protein FLJ10097       37230_at   down   0.070461   KIAA0469 gene product       39717_g_at   down   0.07051   mitochondrial ribosomal protein L33       35793_at   down   0.07062   Ras-GTPase activating protein SH3 domain-binding                   protein 2       39633_at   up   0.070855   S100 calcium binding protein A3       35923_at   up   0.070865   cholecystokinin B receptor       32615_at   down   0.070887   aspartyl-tRNA synthetase       40761_at   down   0.071214   solute carrier family 16 (monocarboxylic acid                   transporters), member 5       32108_at   up   0.071219   sepiapterin reductase (7,8-dihydrobiopterin:NADP+                   oxidoreductase)       38392_at   down   0.071227   actin related protein 2/3 complex, subunit 5, 16 kDa       35275_at   up   0.071315   adaptor-related protein complex 1, gamma 1 subunit       AFFX-   up   0.07143       hum_alu_at       35527_at   up   0.071458   calcium channel, voltage-dependent, alpha 2/delta subur 1       34752_at   down   0.071628   NIMA (never in mitosis gene a)-related kinase 7       35634_at   down   0.071647   mitogen-activated protein kinase kinase kinase 7                   interacting protein 1       36452_at   up   0.071789   synaptopodin       35975_at   down   0.071826   myeloid/lymphoid or mixed-lineage leukemia (trithorax                   homolog,  Drosophila ); translocated to, 3       33707_at   up   0.071894   phospholipase A2, group IVC (cytosolic, calcium-                   independent)       34274_at   down   0.071954   RNA binding motif protein 16       40282_s_at   up   0.071967   D component of complement (adipsin)       40929_at   down   0.072007   SOCS box-containing WD protein SWiP-1       37024_at   down   0.072145   lipopolysaccharide-induced TNF factor       1005_at   up   0.072186   dual specificity phosphatase 1       38968_at   up   0.072257   SH3-domain binding protein 5 (BTK-associated)       34013_f_at   up   0.072278   POU domain, class 1, transcription factor 1 (Pit1, growth                   hormone factor 1)       33867_s_at   down   0.072333   RNA binding motif, single stranded interacting protein 1       38096_f_at   down   0.072339   major histocompatibility complex, class II, DP beta 1       37657_at   up   0.072576   paralemmin       33388_at   up   0.072624   testis expressed gene 261       39561_at   up   0.072667   chromobox homolog 6       34578_at   up   0.072676   sarcoglycan, gamma (35 kDa dystrophin-associated                   glycoprotein)       40458_at   down   0.072706   signal transducer and activator of transcription 5A       934_at   up   0.072711   glycosylphosphatidylinositol specific phospholipase D1       36875_at   down   0.072713   inhibitor of Bruton&#39;s tyrsoine kinase       35526_at   up   0.07279   complement component 9       38359_at   up   0.072822   RAS guanyl releasing protein 2 (calcium and DAG-                   regulated)       41156_g_at   down   0.072839   catenin (cadherin-associated protein), alpha 1, 102 kDa       37000_at   down   0.072839   DKFZP564B167 protein       450_g_at   down   0.072846   cell growth regulatory with ring finger domain       38892_at   down   0.072861   KIAA0240 protein       33224_at   up   0.072965   cysteine and histidine rich 1       33646_g_at   up   0.073003   GM2 ganglioside activator protein       31667_r_at   up   0.073068   nuclear receptor subfamily 2, group E, member 3       32853_at   down   0.073154   translocase of outer mitochondrial membrane 70 homolo                   A (yeast)       34193_at   up   0.073157   cell adhesion molecule with homology to L1CAM (close                   homolog of L1)       36017_at   up   0.073176   chromosome 13 open reading frame 1       36110_at   down   0.073203   RAB5A, member RAS oncogene family       37861_at   up   0.073269   CD1E antigen, e polypeptide       41826_at   up   0.073366   KIAA1467 protein       31682_s_at   up   0.073398   chondroitin sulfate proteoglycan 2 (versican)       34389_at   up   0.073463   collagen, type XIV, alpha 1 (undulin)       33627_at   up   0.073511   phosphoinositide-3-kinase, catalytic, delta polypeptide       37238_s_at   up   0.07355   membrane-associated tyrosine- and threonine-specific                   cdc2-inhibitory kinase       39167_r_at   down   0.073633   serine (or cysteine) proteinase inhibitor, clade H (heat                   shock protein 47), member 1, (collagen binding protein 1       38735_at   up   0.073757   KIAA0513 gene product       38477_at   down   0.073758   diptheria toxin resistance protein required for diphthamid                   biosynthesis-like 1 ( S. cerevisiae )       36399_at   up   0.073791   pre-mRNA splicing SR protein rA4       40150_at   down   0.074001   small nuclear ribonucleoprotein D3 polypeptide 18 kDa       40276_at   down   0.074021   proteasome (prosome, macropain) 26S subunit, non-                   ATPase, 7 (Mov34 homolog)       31948_at   down   0.07403   ribosomal protein S21       34269_at   down   0.074059   erythroid differentiation-related factor 1       1568_s_at   down   0.074061   interferon (alpha, beta and omega) receptor 2       33242_at   down   0.074072   hypothetical protein DT1P1A10       31967_at   up   0.074076   nephrosis 1, congenital, Finnish type (nephrin)       40167_s_at   down   0.074152   likely ortholog of mouse WD-40-repeat-containing protei                   with a SOCS box 2       35766_at   down   0.074163   keratin 18       41553_at   up   0.074209   chromosome 8 open reading frame 1       755_at   down   0.07422   inositol 1,4,5-triphosphate receptor, type 1       34697_at   up   0.074223   low density lipoprotein receptor-related protein 6       38271_at   down   0.074257   histone deacetylase 4       32629_f_at   up   0.074409   butyrophilin, subfamily 3, member A1       40263_at   up   0.074575   zinc finger protein-like 1       34357_g_at   down   0.074581   SRB7 suppressor of RNA polymerase B homolog (yeast)       AFFX-BioB-M_at   up   0.074593       36507_at   up   0.074761   zinc finger protein 282       37377_i_at   up   0.074824   lamin A/C       39381_at   down   0.074885   PHD finger protein 10       38374_at   down   0.074924   TGFB inducible early growth response       32961_at   down   0.075047   c-myc promoter-binding protein       38219_at   down   0.075065   v-crk sarcoma virus CT10 oncogene homolog (avian)       40517_at   down   0.075102   KIAA0372 gene product       40825_at   up   0.075117   microtubule-associated protein, RP/EB family, member 3       35208_at   down   0.075192   KIAA0874 protein       37521_s_at   down   0.075228   nucleolar cysteine-rich protein       37173_at   up   0.07526   centromere protein E, 312 kDa       31738_at   up   0.075288       38071_at   down   0.075384   heterogeneous nuclear ribonucleoprotein F       33285_i_at   down   0.075391   hypothetical protein FLJ21168       153_f_at   up   0.075466   histone 1, H2bj       32734_at   down   0.075516   protein phosphatase 2, regulatory subunit B (B56), epsilo                   isoform       39360_at   down   0.07553   sorting nexin 3       39509_at   down   0.07559   programmed cell death 4 (neoplastic transformation                   inhibitor)       39852_at   down   0.075598   spastic paraplegia 20, spartin (Troyer syndrome)       32333_at   up   0.075602       36535_at   down   0.075653   microfibrillar-associated protein 1       39780_at   down   0.075735   protein phosphatase 3 (formerly 2B), catalytic subunit,                   beta isoform (calcineurin A beta)       35488_at   down   0.075738   small nuclear RNA activating complex, polypeptide 1,                   43 kDa       545_g_at   down   0.075781   nuclear factor of kappa light polypeptide gene enhancer                   B-cells 2 (p49/p100)       41711_at   up   0.075904   thioredoxin reductase 2       34613_at   up   0.075912   KIAA1086 protein       33831_at   down   0.07592   CREB binding protein (Rubinstein-Taybi syndrome)       31797_at   down   0.075936   TBP-like 1       34548_at   up   0.075953   cytochrome P450, family 11, subfamily B, polypeptide 1       37030_at   down   0.076042   expressed in T-cells and eosinophils in atopic dermatitis       845_at   up   0.076077   signal transducer and activator of transcription 6,                   interleukin-4 induced       39253_s_at   down   0.076112   v-ral simian leukemia viral oncogene homolog A (ras                   related)       1821_at   down   0.076123       41777_at   down   0.07617   ATPase, H+ transporting, lysosomal interacting protein 2       34457_at   up   0.076243   solute carrier family 30 (zinc transporter), member 3       41061_at   down   0.076272   huntingtin interacting protein 1       34829_at   up   0.076322   dyskeratosis congenita 1, dyskerin       35751_at   down   0.076335   succinate dehydrogenase complex, subunit B, iron sulfur                   (Ip)       35396_at   up   0.076518   hyaluronan synthase 2       39420_at   down   0.076789   DNA-damage-inducible transcript 3       100_g_at   up   0.076854   Rab geranylgeranyltransferase, alpha subunit       33863_at   up   0.076937   hypoxia up-regulated 1       36980_at   down   0.076989   proline rich 2       41736_g_at   up   0.077002   KIAA0870 protein       40148_at   down   0.077005   amyloid beta (A4) precursor protein-binding, family B,                   member 2 (Fe65-like)       36216_at   down   0.077027   sorting nexin 4       33656_at   down   0.077078   ribosomal protein L37       135_g_at   down   0.077114   abl-interactor 2       41512_at   down   0.077118   BRCA1 associated protein       1451_s_at   up   0.07736   osteoblast specific factor 2 (fasciclin I-like)       36224_g_at   down   0.077412   splicing factor proline/glutamine rich (polypyrimidine trac                   binding protein associated)       31903_at   up   0.077415   synovial sarcoma translocation gene on chromosome 18                   like 1       33632_g_at   down   0.077589   similar to  S. pombe  dim1+       40625_f_at   up   0.07767   metaxin 1       37541_at   up   0.077734   selectin P ligand       692_s_at   up   0.077795   superoxide dismutase 3, extracellular       34259_at   up   0.07782   KIAA0664 protein       32871_at   up   0.077851       41806_at   up   0.077878   fibroblast growth factor 2 (basic)       40961_at   down   0.077885   SWI/SNF related, matrix associated, actin dependent                   regulator of chromatin, subfamily a, member 2       35671_at   up   0.077932   general transcription factor IIIC, polypeptide 1, alpha                   220 kDa       40379_at   up   0.077985   cytochrome P450, family 2, subfamily E, polypeptide 1       37163_at   down   0.077986   DKFZP586C1619 protein       33619_at   down   0.078048   ribosomal protein S13       424_s_at   up   0.07813   fibroblast growth factor receptor 1 (fms-related tyrosine                   kinase 2, Pfeiffer syndrome)       31758_at   up   0.07818       38779_r_at   up   0.078277   hepatoma-derived growth factor (high-mobility group                   protein 1-like)       38102_at   down   0.078302   hypothetical protein FLJ34588       32768_at   up   0.078331   tudor domain containing 3       33659_at   up   0.078352   cofilin 1 (non-muscle)       36374_at   up   0.078482       38006_at   down   0.078527   CD48 antigen (B-cell membrane protein)       38927_i_at   up   0.078558   tyrosinase (oculocutaneous albinism IA)       36094_at   up   0.078582   troponin T3, skeletal, fast       350_at   down   0.078582   zinc finger protein 161       33155_at   up   0.078626   iduronidase, alpha-L-       39315_at   up   0.078642   angiopoietin 1       33162_at   down   0.078765   insulin receptor       1440_s_at   down   0.078833   tumor necrosis factor receptor superfamily, member 6       37566_at   up   0.078937   KIAA1045 protein       40467_at   down   0.079211   succinate dehydrogenase complex, subunit D, integral                   membrane protein       211_at   down   0.079258   down-regulator of transcription 1, TBP-binding (negative                   cofactor 2)       36282_at   up   0.079286       39427_at   down   0.079371   ubiquinol-cytochrome c reductase binding protein       39810_at   down   0.079388   hypothetical protein MGC2749       41824_at   down   0.079408   CGI-48 protein       41508_at   up   0.079432   early growth response 4       1614_s_at   down   0.079473   ubiquitin specific protease 6 (Tre-2 oncogene)       1072_g_at   up   0.079479   GATA binding protein 2       36582_g_at   down   0.079698   glycyl-tRNA synthetase       35105_at   up   0.079724   sciellin       34598_at   up   0.079789   tenascin R (restrictin, janusin)       35154_at   up   0.079876   BTB (POZ) domain containing 2       40290_f_at   down   0.080058   sialyltransferase 4A (beta-galactoside alpha-2,3-                   sialyltransferase)       34201_at   down   0.080202   DnaJ (Hsp40) homolog, subfamily A, member 2       40870_g_at   down   0.08021   RNA binding motif protein 6       36610_at   down   0.080302   R3H domain (binds single-stranded nucleic acids)                   containing       36155_at   up   0.080485   sparc/osteonectin, cwcv and kazal-like domains                   proteoglycan (testican) 2       33209_at   down   0.080629   YY1 transcription factor       40887_g_at   up   0.080665   eukaryotic translation elongation factor 1 alpha 1       617_at   down   0.080689   acid phosphatase, prostate       35214_at   up   0.080736   UDP-glucose dehydrogenase       916_at   up   0.080801   protein tyrosine phosphatase, receptor type, N       40279_at   up   0.080847   KIAA0121 gene product       38712_at   down   0.080849   chromosome 1 open reading frame 9       41120_at   up   0.080863   aminomethyltransferase (glycine cleavage system prote                   T)       37813_at   up   0.08087       1486_at   up   0.080961   polymerase (RNA) II (DNA directed) polypeptide J,                   13.3 kDa       34351_at   up   0.081014   phospholipase C, gamma 1 (formerly subtype 148)       34809_at   down   0.081037   KIAA0999 protein       39040_at   down   0.081117   ubiquitin-conjugating enzyme E2, J1 (UBC6 homolog,                   yeast)       40689_at   down   0.081186   sel-1 suppressor of lin-12-like ( C. elegans )       931_at   down   0.081247   Epstein-Barr virus induced gene 2 (lymphocyte-specific                   protein-coupled receptor)       39147_g_at   up   0.081251   alpha thalassemia/mental retardation syndrome X-linked                   (RAD54 homolog,  S. cerevisiae )       38116_at   down   0.08134   KIAA0101 gene product       1682_s_at   up   0.081428   ATP-binding cassette, sub-family B (MDR/TAP), membe 1       36519_at   down   0.081516   excision repair cross-complementing rodent repair                   deficiency, complementation group 1 (includes                   overlapping antisense sequence)       40294_at   up   0.081521   ATP-binding cassette, sub-family B (MDR/TAP), membe 9       38567_at   down   0.081526   CD1D antigen, d polypeptide       160029_at   down   0.081576   protein kinase C, beta 1       195_s_at   down   0.081607   caspase 4, apoptosis-related cysteine protease       36748_at   up   0.081853   synapsin II       475_at   up   0.081884   receptor (TNFRSF)-interacting serine-threonine kinase 1       31423_at   up   0.081988       35907_at   up   0.081994   cyclin F       39033_at   down   0.082005   chromosome 1 open reading frame 8       31734_at   up   0.082019   homeo box C11       32640_at   up   0.082173   intercellular adhesion molecule 1 (CD54), human                   rhinovirus receptor       39498_at   up   0.082268   FXYD domain containing ion transport regulator 2       1253_at   down   0.082282   glycogen synthase kinase 3 beta       33435_r_at   down   0.082325   BET1 homolog ( S. cerevisiae )       35810_at   down   0.082362   actin related protein 2/3 complex, subunit 3, 21 kDa       33964_at   up   0.082441   crystallin, gamma C       40866_at   down   0.082452   nipsnap homolog 1 ( C. elegans )       37045_at   down   0.082479   sorting nexin 19       39431_at   down   0.082604   aminopeptidase puromycin sensitive       38514_at   down   0.082742   immunoglobulin lambda-like polypeptide 1       33876_at   up   0.082748   transcriptional co-activator with PDZ-binding motif (TAZ)       882_at   up   0.082785   colony stimulating factor 1 (macrophage)       34123_at   up   0.082836       34533_at   up   0.082873   hypothetical protein FLJ32746       33543_s_at   down   0.082933   pinin, desmosome associated protein       37980_at   down   0.082971   CBF1 interacting corepressor       574_s_at   down   0.083007   caspase 1, apoptosis-related cysteine protease                   (interleukin 1, beta, convertase)       789_at   up   0.083148   early growth response 1       34163_g_at   down   0.083192   RNA binding protein with multiple splicing       39718_r_at   down   0.083273   mitochondrial ribosomal protein L33       1136_at   down   0.083343   deoxythymidylate kinase (thymidylate kinase)       33893_r_at   down   0.08337   KARP-1-binding protein       40673_at   up   0.083476   acyl-Coenzyme A dehydrogenase, short/branched chain       36872_at   down   0.08356   cyclic AMP phosphoprotein, 19 kD       31930_f_at   up   0.083573   Rhesus blood group, CcEe antigens       40119_at   down   0.083591   cartilage associated protein       241_g_at   up   0.083623   spermidine synthase       519_g_at   up   0.083723   nuclear receptor subfamily 1, group H, member 2       37827_r_at   down   0.083832   chromosome 21 open reading frame 5       37679_at   down   0.083856   interferon-related developmental regulator 1       37385_at   down   0.08386   peptidyl-prolyl isomerase G (cyclophilin G)       33760_at   down   0.083864   peroxisomal biogenesis factor 14       671_at   up   0.083879   secreted protein, acidic, cysteine-rich (osteonectin)       35143_at   down   0.083893   hypothetical protein DKFZp566A1524       35946_at   up   0.083985   NEL-like 1 (chicken)       34678_at   down   0.084027   fer-1-like 3, myoferlin ( C. elegans )       36121_at   up   0.084131   epsin 2       35413_s_at   up   0.084141   zinc finger protein 22 (KOX 15)       41197_at   down   0.084209   RAD23 homolog A ( S. cerevisiae )       32173_at   up   0.084294   translational inhibitor protein p14.5       39791_at   down   0.084465   ATPase, Ca++ transporting, cardiac muscle, slow twitch       41124_r_at   down   0.084468   ectonucleotide pyrophosphatase/phosphodiesterase 2                   (autotaxin)       41573_at   down   0.08456   Sp3 transcription factor       31805_at   up   0.084593   fibroblast growth factor receptor 3 (achondroplasia,                   thanatophoric dwarfism)       33080_s_at   up   0.084607   RAP1, GTPase activating protein 1       109_at   down   0.084611   Rab9 effector p40       34270_at   up   0.084688   LSM5 homolog, U6 small nuclear RNA associated ( S. cerevisiae )       37406_at   down   0.084705   microtubule-associated protein, RP/EB family, member 2       664_at   down   0.08478   interleukin 8 receptor, beta       36350_at   up   0.084859       32883_at   down   0.084885   KRAB zinc finger protein KR18       35901_at   up   0.08489   piwi-like 1 ( Drosophila )       1885_at   up   0.084893   excision repair cross-complementing rodent repair                   deficiency, complementation group 3 (xeroderma                   pigmentosum group B complementing)       40701_at   up   0.085053   ubiquitin specific protease 13 (isopeptidase T-3)       268_at   down   0.085065   platelet/endothelial cell adhesion molecule (CD31 antige       1845_at   down   0.085084   mitogen-activated protein kinase kinase 4       41813_at   up   0.085175   nucleoporin 210       37282_at   down   0.085322   MAD2 mitotic arrest deficient-like 1 (yeast)       39883_at   down   0.085337   putative dimethyladenosine transferase       39581_at   down   0.085337   cystatin A (stefin A)       40558_at   up   0.085339   guanylate cyclase activator 1B (retina)       1143_s_at   down   0.085382       37796_at   up   0.085405   leucine rich repeat neuronal 4       40758_at   down   0.085415   immature colon carcinoma transcript 1       AFFX-   up   0.0855       M27830_3_at       36462_at   up   0.085538   SMYD family member 5       31853_at   down   0.08559   embryonic ectoderm development       37293_at   down   0.085666   KIAA0097 gene product       38705_at   down   0.085669   ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog,                   yeast)       37588_s_at   up   0.085678   mitogen-activated protein kinase 8 interacting protein 2       40211_at   down   0.08573   heterogeneous nuclear ribonucleoprotein A1       467_at   down   0.08595   osteoclast stimulating factor 1       38530_at   up   0.086109   hypothetical protein FLJ22709       40048_at   down   0.086249   pumilio homolog 1 ( Drosophila )       34223_at   up   0.086252   colony stimulating factor 3 receptor (granulocyte)       33240_at   up   0.0863   likely ortholog of mouse semaF cytoplasmic domain                   associated protein 3       33886_at   down   0.086302   spectrin SH3 domain binding protein 1       39832_at   up   0.086357   arsenate resistance protein ARS2       31638_at   up   0.086423       41814_at   down   0.086559   fucosidase, alpha-L-1, tissue       31800_at   up   0.086561       31979_at   up   0.086615   6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4       34961_at   up   0.086616   T cell activation, increased late expression       35597_at   up   0.086723   phosphoprotein regulated by mitogenic pathways       33529_at   up   0.086755   alcohol dehydrogenase 7 (class IV), mu or sigma                   polypeptide       38889_at   up   0.086863   MAD, mothers against decapentaplegic homolog                   ( Drosophila ) interacting protein, receptor activation anc       39221_at   down   0.086888   leukocyte immunoglobulin-like receptor, subfamily B (wi                   TM and ITIM domains), member 2       32443_at   up   0.087   zinc finger protein 157 (HZF22)       34011_at   up   0.08701   harakiri, BCL2 interacting protein (contains only BH3                   domain)       39643_at   up   0.087011   polymerase (DNA directed), gamma 2, accessory subur       37935_at   up   0.08708   PRP4 pre-mRNA processing factor 4 homolog (yeast)       39749_at   down   0.087136   proteasome (prosome, macropain) 26S subunit, non-                   ATPase, 4       36865_at   down   0.08718   KIAA0759 protein       36081_s_at   down   0.087181   chromosome 21 open reading frame 18       38347_at   down   0.087211   elongation protein 4 homolog ( S. cerevisiae )       485_at   up   0.087219       1001_at   up   0.087263   tyrosine kinase with immunoglobulin and epidermal                   growth factor homology domains       35293_at   down   0.087479   Sjogren syndrome antigen A2 (60 kDa, ribonucleoprotein                   autoantigen SS-A/Ro)       40733_f_at   up   0.087601   msh homeo box homolog 2 ( Drosophila )       34474_at   down   0.087639       41420_at   down   0.087753   insulin-like growth factor binding protein 5       210_at   up   0.08778   phospholipase C, beta 2       40901_at   down   0.087859   striatin, calmodulin binding protein 3       34708_at   up   0.087884   ficolin (collagen/fibrinogen domain containing) 3 (Hakata                   antigen)       1671_s_at   up   0.087925   mitogen-activated protein kinase 14       33165_at   down   0.087974   target of EGR1, member 1 (nuclear)       31679_at   up   0.087997       39290_f_at   up   0.088024   PAI-1 mRNA-binding protein       40480_s_at   down   0.088156   FYN oncogene related to SRC, FGR, YES       953_g_at   down   0.088165       35845_at   down   0.088184   SEC24 related gene family, member B ( S. cerevisiae )       41125_r_at   up   0.088253   ectonucleotide pyrophosphatase/phosphodiesterase 2                   (autotaxin)       32190_at   down   0.088305   fatty acid desaturase 2       41117_s_at   up   0.088317   solute carrier family 9 (sodium/hydrogen exchanger),                   isoform 3 regulatory factor 2       39824_at   up   0.088333   protein tyrosine phosphatase type IVA, member 3       38237_at   up   0.088414   gamma-glutamyltransferase-like activity 1       31713_s_at   up   0.088448   discs, large ( Drosophila ) homolog-associated protein 2       37323_r_at   up   0.088637   hydroxyprostaglandin dehydrogenase 15-(NAD)       39862_at   up   0.088689   KIAA0296 gene product       31594_at   up   0.088804   keratin, hair, acidic, 3A       33272_at   up   0.088835   serum amyloid A1       38907_at   up   0.088895       32927_at   down   0.088975       41425_at   down   0.089008   Friend leukemia virus integration 1       39396_at   down   0.089017   lysophospholipase I       34858_at   up   0.089029   potassium channel tetramerisation domain containing 2       32067_at   up   0.089124   cAMP responsive element modulator       35473_at   up   0.08921   collagen, type I, alpha 1       38073_at   down   0.089213   RNA (guanine-7-) methyltransferase       34859_at   up   0.089268   melanoma antigen, family D, 2       38048_at   up   0.089393   RNA binding protein with multiple splicing       38061_at   up   0.08946   ribosomal protein S16       34671_at   down   0.08955   polymerase (RNA) III (DNA directed) (62 kD)       32813_s_at   up   0.089623   katanin p80 (WD repeat containing) subunit B 1       39829_at   up   0.089659   ADP-ribosylation factor-like 7       34736_at   up   0.089693   cyclin B1       40515_at   down   0.08972   eukaryotic translation initiation factor 2B, subunit 2 beta,                   39 kDa       37763_at   up   0.089731   retinoid X receptor, beta       33984_at   up   0.089752   heat shock 90 kDa protein 1, beta       32025_at   down   0.089771   transcription factor 7-like 2 (T-cell specific, HMG-box)       38990_at   down   0.089788   F-box only protein 9       38117_at   up   0.089832   SEC24 related gene family, member C ( S. cerevisiae )       36784_at   down   0.090005   chorionic somatomammotropin hormone-like 1       32662_at   up   0.090014   mediator of DNA damage checkpoint 1       41535_at   down   0.090077   CDK2-associated protein 1       39152_f_at   down   0.0901   coilin       2069_s_at   down   0.090137   catenin (cadherin-associated protein), alpha 1, 102 kDa       35307_at   down   0.090206   GDP dissociation inhibitor 2       35783_at   down   0.090268   vesicle-associated membrane protein 3 (cellubrevin)       909_g_at   down   0.090304   interferon-induced protein with tetratricopeptide repeats:       34038_at   up   0.090364   solute carrier family 6 (neurotransmitter transporter,                   GABA), member 13       37723_at   down   0.090364   cyclin G2       39913_at   up   0.090436   heparan sulfate 6-O-sulfotransferase 1       36511_at   down   0.09055   SAC1 suppressor of actin mutations 1-like (yeast)       31846_at   up   0.090573   ras homolog gene family, member D       38419_at   down   0.090574   KIAA0196 gene product       1745_at   down   0.090606       34680_s_at   down   0.090628   KIAA0107 gene product       31833_at   up   0.090658   phosphatidylinositol-4-phosphate 5-kinase, type I, alpha       39385_at   up   0.090659   alanyl (membrane) aminopeptidase (aminopeptidase N,                   aminopeptidase M, microsomal aminopeptidase, CD13,                   p150)       37768_at   up   0.0908   N-methylpurine-DNA glycosylase       34161_at   up   0.090915   lactoperoxidase       41868_at   up   0.090976   gamma-glutamyltransferase 1       37940_f_at   up   0.090998   apolipoprotein B mRNA editing enzyme, catalytic                   polypeptide-like 3C       35230_at   up   0.091025   TIR domain containing adaptor inducing interferon-beta       40107_at   up   0.091064   aldolase C, fructose-bisphosphate       40764_at   up   0.091092   glutamic-oxaloacetic transaminase 2, mitochondrial                   (aspartate aminotransferase 2)       37685_at   down   0.091314   phosphatidylinositol binding clathrin assembly protein       1288_s_at   up   0.091336   eukaryotic translation elongation factor 1 alpha 1       33379_at   up   0.09136   synovial sarcoma, X breakpoint 2 interacting protein       39641_at   up   0.091498   uracil-DNA glycosylase 2       38739_at   down   0.091509   v-ets erythroblastosis virus E26 oncogene homolog 2                   (avian)       35807_at   up   0.091617   cytochrome b-245, alpha polypeptide       36213_at   up   0.09167   malignant fibrous histiocytoma amplified sequence 1       31522_f_at   up   0.091671   histone 1, H2bf       36184_at   up   0.091691   procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine                   hydroxylase, Ehlers-Danlos syndrome type VI)       806_at   up   0.091752   cytokine-inducible kinase       2081_s_at   down   0.091827   protein kinase C, theta       37621_at   down   0.091829   interleukin 6 signal transducer (gp130, oncostatin M                   receptor)       41334_r_at   down   0.091888       36613_at   up   0.092021   interferon-related developmental regulator 2       32878_f_at   down   0.09204       34908_at   up   0.092066   hypothetical protein FLJ13946       37212_at   up   0.0921   Sp2 transcription factor       2084_s_at   up   0.092203   ets variant gene 4 (E1A enhancer binding protein, E1AF       32856_at   up   0.092236   KIAA0819 protein       39219_at   down   0.092383   CCAAT/enhancer binding protein (C/EBP), gamma       37053_at   up   0.092455   ATPase, Ca++ transporting, plasma membrane 2       38962_at   up   0.092537   KIAA0298 gene product       36624_at   up   0.092613   IMP (inosine monophosphate) dehydrogenase 2       40757_at   up   0.092646   granzyme A (granzyme 1, cytotoxic T-lymphocyte-                   associated serine esterase 3)       31780_f_at   up   0.092646       37438_at   up   0.092667   KIAA0419 gene product       35844_at   up   0.092675   syndecan 4 (amphiglycan, ryudocan)       AFFX-BioB-M_st   up   0.092696       38695_at   down   0.092773   NADH dehydrogenase (ubiquinone) Fe—S protein 4,                   18 kDa (NADH-coenzyme Q reductase)       31446_s_at   up   0.092903   proline rich 5 (salivary)       32747_at   down   0.092991   aldehyde dehydrogenase 2 family (mitochondrial)       32129_at   down   0.093034   zinc finger protein 364       37998_at   up   0.093081   superkiller viralicidic activity 2-like ( S. cerevisiae )       40944_at   down   0.09309   TGFB inducible early growth response 2       31512_at   up   0.093117   immunoglobulin kappa variable 1-13       41268_g_at   down   0.093129   KIAA1049 protein       31960_f_at   up   0.093132   G antigen 2       2009_at   up   0.093184   PTK2B protein tyrosine kinase 2 beta       37520_at   down   0.093259   nucleolar cysteine-rich protein       32300_s_at   up   0.09328   tyrosine hydroxylase       36837_at   up   0.093336   kinesin family member 2C       39834_at   up   0.093358   cholinergic receptor, nicotinic, epsilon polypeptide       40465_at   down   0.09338   prp28, U5 snRNP 100 kd protein       33965_at   up   0.093408   chemokine (C—C motif) ligand 1       41068_at   down   0.09347   outer dense fiber of sperm tails 2       35100_at   up   0.093484   sialyltransferase 8C (alpha2,3Galbeta1,4GlcNAcalpha                   2,8-sialyltransferase)       38171_at   up   0.093582   WD-repeat protein       34101_at   up   0.093618       35279_at   down   0.09364   Tax1 (human T-cell leukemia virus type I) binding protein 1       34129_at   up   0.093741   tomosyn-like       38081_at   down   0.093785   leukotriene A4 hydrolase       33923_s_at   down   0.09381   PR domain containing 2, with ZNF domain       39965_at   up   0.093868   ras-related C3 botulinum toxin substrate 3 (rho family,                   small GTP binding protein Rac3)       40691_at   down   0.093908   zinc finger protein 274       35562_at   up   0.093917   histone 1, H2bj       40853_at   down   0.093992   ATPase, Class V, type 10D       34112_r_at   up   0.094039       1073_at   down   0.094039   transcription elongation factor A (SII), 1       37535_at   down   0.094144   cAMP responsive element binding protein 1       32140_at   up   0.094211   sortilin-related receptor, L(DLR class) A repeats-                   containing       33077_at   up   0.094215       34028_at   down   0.094218   G protein-coupled receptor 19       35356_at   down   0.094405   hypothetical protein MGC9651       40797_at   down   0.094519   a disintegrin and metalloproteinase domain 10       38569_at   up   0.094591   nuclear respiratory factor 1       1715_at   down   0.094642   tumor necrosis factor (ligand) superfamily, member 10       36277_at   up   0.094818   CD3E antigen, epsilon polypeptide (TiT3 complex)       34529_at   up   0.094849       35445_at   up   0.0949   sorting nexin 26       32879_at   down   0.094954       41635_at   down   0.094971   Wilms tumor 1 associated protein       38673_s_at   down   0.094985   cyclin-dependent kinase inhibitor 1C (p57, Kip2)       37118_at   up   0.095049   ret finger protein-like 1 antisense       35306_at   down   0.095212   DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 15       40992_s_at   down   0.09541   sin3-associated polypeptide, 30 kDa       37891_at   up   0.095425       39448_r_at   up   0.095584   B7 gene       38843_at   down   0.095688   high-mobility group protein 2-like 1       39224_at   down   0.0957   centaurin, delta 1       39143_at   down   0.095718   nuclear factor of activated T-cells, cytoplasmic,                   calcineurin-dependent 1       39985_r_at   up   0.095724   FKBP-associated protein       38592_s_at   up   0.095754   KIAA0284 protein       1518_at   up   0.095784   v-ets erythroblastosis virus E26 oncogene homolog 1                   (avian)       35605_at   up   0.095808   angiopoietin-like factor       41712_at   down   0.095851   likely ortholog of mouse aquarius       35999_r_at   down   0.095865   KIAA0781 protein       36735_f_at   up   0.09588   killer cell immunoglobulin-like receptor, three domains,                   long cytoplasmic tail, 2       33710_at   down   0.095883   putative protein similar to nessy ( Drosophila )       32888_at   up   0.095889   leukocyte tyrosine kinase       37397_at   down   0.095893   platelet/endothelial cell adhesion molecule (CD31 antige       41528_at   up   0.095958       40766_at   up   0.096077   complement component 4A       36389_at   down   0.096078   class-I MHC-restricted T cell associated molecule       39666_at   up   0.096165   guanine nucleotide binding protein (G protein), gamma 4       34755_at   up   0.096176   ADP-ribosyltransferase (NAD+; poly(ADP-ribose)                   polymerase)-like 2       32708_g_at   down   0.096177   katanin p60 (ATPase-containing) subunit A 1       32228_at   up   0.096212   adaptor-related protein complex 2, alpha 2 subunit       40886_at   down   0.09626   eukaryotic translation elongation factor 1 alpha 1       32285_g_at   up   0.096383   T-box 1       39734_at   down   0.096467   small inducible cytokine subfamily E, member 1                   (endothelial monocyte-activating)       31337_at   up   0.096538   gonadotropin-releasing hormone 2       41488_at   down   0.096667   hypothetical protein A-211C6.1       34438_at   up   0.096753   serine (or cysteine) proteinase inhibitor, clade B                   (ovalbumin), member 9       31478_at   up   0.096764   pancreatic elastase IIB       39867_at   up   0.09692   Tu translation elongation factor, mitochondrial       41324_g_at   up   0.096963   forkhead box M1       1775_at   up   0.097235   polymerase (DNA-directed), alpha (70 kD)       32391_g_at   down   0.097269       40803_at   down   0.097361   pro-oncosis receptor inducing membrane injury gene       34677_f_at   down   0.097379   TL132 protein       493_at   up   0.097484   casein kinase 1, delta       37870_at   up   0.097488   transcription termination factor, RNA polymerase II       41859_at   up   0.097578   uronyl-2-sulfotransferase       37618_at   up   0.097661   homeo box B7       33453_at   up   0.097774   ATPase, H+ transporting, lysosomal interacting protein 1       32909_at   up   0.097796   aquaporin 5       38622_at   up   0.097851   hypothetical protein BC004409       40845_at   down   0.097859   interleukin enhancer binding factor 3, 90 kDa       39351_at   down   0.097885   CD59 antigen p18-20 (antigen identified by monoclonal                   antibodies 16.3A5, EJ16, EJ30, EL32 and G344)       33341_at   down   0.097943   guanine nucleotide binding protein (G protein), beta                   polypeptide 1       38279_at   up   0.098024   guanine nucleotide binding protein (G protein), alpha z                   polypeptide       41543_at   up   0.098055   lymphoid nuclear protein related to AF4       41163_at   down   0.09819   integral type I protein       32101_at   down   0.098215   galactosamine (N-acetyl)-6-sulfate sulfatase (Morquio                   syndrome, mucopolysaccharidosis type IVA)       33172_at   up   0.098326   hypothetical protein FLJ10849       36168_at   up   0.098482   fibroblast growth factor receptor 1 (fms-related tyrosine                   kinase 2, Pfeiffer syndrome)       41385_at   down   0.098533   erythrocyte membrane protein band 4.1-like 3       31537_at   up   0.098538   ADP-ribosyltransferase 1       32564_at   down   0.098647   protein translocation complex beta       1922_g_at   up   0.098667       158_at   down   0.098748   DnaJ (Hsp40) homolog, subfamily B, member 4       857_at   down   0.099054   protein phosphatase 1A (formerly 2C), magnesium-                   dependent, alpha isoform       34029_at   up   0.099115   dentin matrix acidic phosphoprotein       34544_at   down   0.099119   zinc finger protein 267       35348_at   down   0.099122   protein kinase, AMP-activated, beta 1 non-catalytic                   subunit       1075_f_at   up   0.099205   interferon, alpha 16       960_g_at   down   0.099331       35091_at   up   0.099335   neuregulin 2       40785_g_at   down   0.099423   protein phosphatase 2, regulatory subunit B (B56),                   gamma isoform       1921_at   up   0.099462       666_at   up   0.099504   phosphodiesterase 4A, cAMP-specific                   (phosphodiesterase E2 dunce homolog,  Drosophila )       33340_at   down   0.099814   praja 2, RING-H2 motif containing       31759_at   up   0.099864   alpha-2 macroglobulin family protein VIP                  
 
     Example 2  
     Psychiatric Illness Diagnosis with Multigene Expression Classification  
     Patient and Control Subject Recruitment and Study Procedure  
      All subject recruitment was performed according to IRB regulations.  
      Medicated Schizophrenia (SZ) Subjects. Seven White SZ men between the ages of 25-65 were recruited from the residents of a psychiatric center and four community residential facilities. SZ patients were screened for inclusion based on SZ diagnosis. Patient records from previous admissions and from other facilities were collected for each subject. Informed consent was obtained on the patient&#39;s resident ward. Charts were screened for neuroleptic history and in addition for medical history and other medication use. The seven SZ patients who were analyzed in the preliminary study had medication profiles that were diverse and included several different classes of atypical and typical neuroleptic medications: Subject 493: Olanzapine, Depakote, Risperidone., Subject 494: Chloral Hydrate, Zyprexa., Subject 495: Loxapine, Benztropine, Seroquel, Vistaril., Subject 535: Clozapine, Artane., Subject 588: Haloperidol, Haloperidol Decanoate, Cogentin, Depakote., Subject 630: Olanzapine, Risperidone., Subject 631: Haloperidol, Clozapine. One patient (ID 494) had been neuroleptic drug-free (Clozapine) a short time (5 days).  
      Non-Medication SZ Subject. One never-medicated 39-year-old White male SZ subject was recruited into the study, Subject 964. Increasing delusions and paranoia precipitated the subject&#39;s admission to a local community hospital. He was hospitalized for 37 days but refused all medications. He was assessed for court-mandated treatment but did not fulfill the criteria of dangerousness and this avenue was not pursued. At no time during his hospitalization was any emergency or stat medication administered. The patient was given an Axis I paranoid schizophrenia diagnosis. His global assessment of functioning score was 28%. The patient&#39;s physical examination found no medical conditions or abnormalities, and his SMAC, CBC and urinalysis results were all within the normal ranges. At admission a urine drug toxicology screen proved negative.  
      Informed consent was obtained, and a blood draw was performed. The subject was questioned about his general health, his treatment history and any drug, alcohol and smoking histories (of which all were negative). A brief psychiatric rating scale (BPRS) was administered and his BPRS score was 43.  
      Control Subjects. Five age-matched controls were recruited from the staff. Subjects completed a form (with the study team assistance) documenting that neither they nor their first degree relatives had a history of SZ, other psychotic disorders, mood disorders or of paranoid, schizoid, or schizotype personality disorder. Subjects were also questioned about their smoking history any current use of, or history of alcohol or illicit drugs. Forms were also completed listing current medications and medical history. Subjects were seen at their place of work and informed consent obtained. Control subjects were given the study ID nos. 401, 492, 536, 634, and 641).  
      BPD Subjects. Two White male subjects with a diagnosis of BPD (both aged 41), were recruited into the study. Patient records from previous admissions and from other facilities were collected for each subject. Informed consent was obtained on the patient&#39;s resident ward. Charts were screened for present and past neuroleptic use and in addition for medical history exclusions and other medication or drug use and smoker status (as described above). The BPD subjects had medication profiles as follows: Subject 767: Depakote, Quietapine and Zoloft., Subject 846: Fluoxetine and Remeron.  
      Medical Exclusions. A list of medical exclusions was generated. A complete blood count (CBC) with differentials was performed for all samples collected 7.  
      Sample Processing and Microarray Hybridization. Immediately after blood collection, leukocytes were isolated by lysis of red cells, centrifugation and washing (Qiagen). Purified leukocytes were stored at −70° C. prior to RNA extraction. 8 μg of total RNA was employed as a cDNA synthesis template, using an oligo-dT primer and Reverse Transcriptase (RT) enzyme, according to standard Affymetrix protocols. Purified cDNA, quantified by gel electrophoresis, was then used as a template to generate biotin labeled cRNA, using an in-vitro transcription kit (Enzo). cRNA samples were quantified by UV spectrometry and stored at −70° C. prior to fragmentation. Following fragmentation, 20 ng of each cRNA product was hybridized to an Affymetrix TEST3 array to check the quality of each sample. Each cRNA sample was then hybridized to an HU95A array.  
      Real-Time RT-PCR. 200 ng of total RNA from each subject was employed for first strand cDNA synthesis, using random hexamer primers and Superscripe II  RT enzyme (Invitrogen). Primers were designed using the Primer3 program (Whitehead Institute), except for the 18S ribosomal RNA primers, which were purchased as an internal standard PCR kit (Ambion). For real-time PCR the SYBR Green assay, which measures the linear binding of florescent molecules to double-stranded DNA molecules at each cycle of the amplification, was performed using the Quantitech Kit (Qiagen), on an ABI PRISM 7700 apparatus. The resultant data was imported into Sequence Detector, v1.7a software (ABI), and Cts were calculated. The Ct (the PCR threshold cycle where an increase in reporter fluorescence above a baseline signal can first be detected) has a direct correlation with template concentration. The Ct&#39;s of samples with known copy numbers were employed to generate standard amplification curves for each set of specific gene primers. Final copy numbers of each sample RNA were determined from a standard curve, and compared with the 18S standard results.  
     Gene Expression Data Acquisition and Analysis  
      Affymetrix® Microarray Suite Software (v5.0) Data acquisition was performed as described for Example 1. The resultant data was converted to Excel spreadsheets, and collated. All gene expression values given an “absent call” were removed from the datasets. Gene expression data was then filtered by removing all genes from analysis if they were not found to be “present” in at least two subjects. All statistical tests on the data were performed in Excel, except those described in detail below.  
      Data analysis and Hierarchical Clustering. Hierarchical clustering was performed as described for Example 1, above, using the Cluster program.  
     Results of the Preliminary Studies  
      Pair-wise Analysis of microarray results. To investigate total sample variability, a pair-wise comparison of expression levels was performed. It is expected that over 12,000 data points, samples should be highly correlated to allow meaningful comparison of the data. Correlation coefficients were within the range of 0.85-0.93 for each comparison (data not shown). Two samples were processed in duplicate by multiple hybridizations to HU95A arrays. The reproducibility of the Affymetrix system was illustrated by the r 2  values of 0.97 and 0.99. For  
      Analysis of gene expression from genes differentially regulated in peripheral blood leukocytes. Genes or protein products previously found to be differentially regulated in blood were investigated. The mean and variance of expression levels were calculated across the SZ and Control groups. Altered expression levels (SZ v Controls for each gene) for the dopamine D 3  receptor (+20%), IL-1 receptor antagonist (+30%), IL-2 (−16%), CD3 (+44%), CD4 (+49%), CD8 (+66%), VLA-4 (+33%) and TNF-α(+185%) were found to concur with previously published findings (Ilani et al., Proc Natl Acad Sci USA 2001; 98(2):625-628; Akiyama. Schizophr Res 1999; 37(1), 97-106; Kim, et al., Biol Psychiatry 1998; 43(9):701-4; Sperner-Unterweger et al., Schizophr Res 1999; 38(1):61-70; Muller et al., Am J Psychiatry 1999; 156(4):634-6; Cazzullo et al., Schizophr Res 1998 31(1):49-55; Naudin et al., Schizophr Res 1997 26(2-3); 227-33). Interestingly, found many groups of genes were found that were more significantly altered between the two subject groups, showing the power of this microarray approach to identify patterns of differentially regulated genes. A few examples of genes that have previously been implicated in studies of SZ or other psychiatric disorders are; neural cell adhesion molecule (N-CAM), +112%, p=0.008, GABA-A receptor, +247%, p=0.0003, L-1 type, calcium channel, +39%, p=0.03, 14-3-3 protein eta chain, −30%, p=0.008, and Ciliary neurotrophic factor, +144%, p=0.005.  
      Hierarchical Clustering of SZ Subjects from Control Subjects. Following filtering of the data, a total of 2635 genes remained for further investigation. It may prove useful to perform a supervised clustering experiment, as surrogate tissue (blood leukocytes) is employed in which differences in the patterns of gene expression from SZ patients compared to control subjects may be more subtle than in tissues such as brain. A two-tailed t-test across the 2695 genes expressed in the subject&#39;s leukocytes was performed, however, for this analysis the non-medicated subject (Subject 964) was not included. Of the original 2695 genes, 513 were found to have expression values significantly different between the SZ subject group and control group (p&lt;0.05), and 948 were found to have p&lt;0.1 between the two groups. Interestingly, an identical t-test on randomized data was performed, where subject samples were randomly placed into one of two groups. This was repeated for multiple permutated datasets, and the mean numbers of differentially regulated genes calculated. 52 genes were found to be significantly different between the randomized groups (p&lt;0.05), while only 122 genes were found to have p&lt;0.1. Thus, randomizing the data results in a vast decrease in the number of genes found to be differentially expressed between subject groups, and may represent the noise of this experimental system. A clustering experiment was implemented on the 948 genes that differentiated between the subject groups (p&lt;0.1, medicated SZ and controls), with the inclusion of subject 964 in this analysis. Expression levels of the 948 genes for each subject (n=13), were input into the cluster program and the results visualized in TreeView.  FIG. 3  shows a partial TreeView figure of the subject cluster results. Two interesting observations were noted, 1) SZ subjects do not appear to cluster based on medication profile, for example, the three SZ subjects receiving Clozapine, (P-494, 535, and 631), do not appear within the same cluster subgroup, while subject 964, a never medicated SZ subject clusters with the SZ group, away from the control subjects, and 2) The smoking status of subjects does not appear to influence the segregation of subjects within the clusters (C-401, 641 and 492 smoke, as do all medicated SZ subjects, but not SZ subject 964). The results of multiple permutations of intra-subject randomization within the data-sets suggesting that these cluster results are not directed by random expression levels in the microarray datasets (data not shown). Preliminary analysis for these studies was performed, and we expect that use of larger subject numbers for each group and a more conservative analysis (p&lt;0.05), will allow further investigation of factors affecting classification of subjects, prior to input into Cluster.  
      Concordance of expression of the Never-Medicated SZ Subject with Medicated SZ Subjects. When subject 964 was added to the SZ patient subject group for significance testing (two-tailed t-tests), versus the healthy control group, there was a 33% increase in the total number of genes that were differentially expressed (p&lt;0.05) between the 2 subject groups, further indicating the concordance of the neuroleptic naive subject with the remainder of the SZ subject group. Additionally, t-testing between the SZ and control subject group, resulted in decreases in p-value (increased significance) for over 79.5% of the genes previously found to be differentially expressed between subject groups prior to the inclusion of subject 964.  
      Analysis of Leukocyte Gene Expression in SZ and Bipolar Disorder (BPD) Subjects. For additional data to support this application to investigate leukocyte gene expression profiles for classification of SZ and BPD, two further subjects were recruited and analyzed with a diagnosis of BPD (using the last of the B/START funds). In addition, we have also recruited one subject with major depression into the study. Although that these numbers are very small, this data supports the hypothesis presented herein, and therefore illustrates the value of continuing this investigation.  
      Analysis of Gene Expression From Genes Differentially Regulated in Peripheral Blood Leukocytes. Expression level data for genes previously found to be differentially regulated in SZ and BPD were investigated. The mean and variance of expression levels were calculated between the groups. Although the data is not statistically significant due to the small subject numbers, transcript levels of TNF-α were ˜100% increased in the SZ versus BPD. Other genes found to be differentially regulated include (SZ v BPD for each gene): IL-1 receptor antagonist (+82%), IL-1 beta (+47%) and dopamine D 3  receptor, (−83%). Many other genes that have also been implicated in psychiatric disorders were found to be differentially expressed between SZ and BPD subjects. For comparison, relative expression of those described above is listed as follows: IL-2 (+92%), CD3 (+42%), CD4 (−25%), CD8 (+36%), N-CAM (+56%), GABA-A receptor (+192%), L-1 type, calcium channel (+32%), 14-3-3 protein eta chain (−79%), and Ciliary neurotrophic factor, (+62%).  
      Hierarchical Clustering of SZ and BPD Subjects. A supervised analysis was then performed using all genes found to be differentially expressed between the SZ and BPD subjects (p&lt;01, n=1002). While this result is not significant, it provides some indication into the likelihood of generating classification profiles when larger subject numbers are employed. The TreeView readout in  FIG. 4A  shows representative samples nodes of similar gene expression (vertical axis), ordered by the total gene expression among the 10 subjects (horizontal axis), where in this example expression levels in the SZ subject samples are lower than in both patients with BPD. The scaled horizontal cluster of subjects ( FIG. 4B ) indicates that distinctive patterns of gene expression can classify subjects into groups as shown by the sub-nodes within the tree diagram. It was observed that based on the overall gene expression of 1002 genes the two BPD patients (BPD-767, 846) clustered into one discrete sub-node away from the SZ patients. Subjects SZ-964 and 495 appears to cluster into a separate branch of the tree when compared to the other SZ subjects, and suggests that the use of additional subjects should allow further investigation of the actual sub-groupings within the subject clusters. To perform a preliminary investigation on this clustering result, subject gene expression levels were randomized within the dataset and the resultant data were re-clustered. One example readout is shown in  FIG. 4 , where intra-subject randomization of the data was performed.  FIG. 5A  shows the TreeView readout from the initial clustering of 1002 genes, as described above.  FIG. 5B  shows the TreeView readout generated following analysis of the randomized dataset. The short branch lengths between each node of the dendrogram imply that following randomization, subjects have overall gene expression patterns very similar to each other. The Cluster analysis of the other random data iterations, resulted in TreeView readouts where either the samples remained in the order of input into Cluster, or alternatively branch lengths were observed to be vastly reduced, indicating very minor differences in overall gene expression between subjects. These results may suggest that the separation of subjects into nodes within the TreeView diagram is not due to random gene expression levels in the microarray datasets.  
      Table 2 shows a list of up- or down-regulated genes from PBLs of the eight schizophrenia subjects.  
               TABLE 2                          Schizophrenia Gene Expression Results       This table includes gene expression profile data from 8 schizophrenic subjects       versus 5 control subjects. The table includes the Affymetrix probe-set ID for the HU95Av2       GeneChip array, and also the EASE assignment. The EASE data were included because       there are instances where an unknown EST (as referenced to by the Affymetrix probeset       ID) has later been characterized by others. However, these curation methods are not 100%       accurate.       It is very important to note that the significance levels for the genes/ESTs can       change with increasing statistical power from comparing additional samples. Therefore, it       may be likely that some genes/ESTs may change in significance.                                 mean                   expression           in           schizophrenic           patients       Affymetrix HU95A   compared to   two tailed       version2 probe set   healthy   Students t-test       ids   controls   significance   EASE Names (david.niaid.nih.gov/david/ease.htm)               37444_at   up   5.39844E−05   par-6 partitioning defective 6 homolog alpha ( C. elegans )       37830_at   up   6.10988E−05   transmembrane 4 superfamily member tetraspan NET-5       1112_g_at   up   6.37745E−05   neural cell adhesion molecule 1       34480_at   up    7.1664E−05   cadherin 16, KSP-cadherin       38736_at   down   0.000100789   WD repeat domain 1       1390_s_at   up   0.000104589   growth hormone releasing hormone       37294_at   down   0.000120464   B-cell translocation gene 1, anti-proliferative       34035_at   up   0.000133975   solute carrier family 10 (sodium/bile acid cotransporter family),                   member 1       33123_at   down   0.000140899   HRIHFB2206 protein       35527_at   up   0.000163856   calcium channel, voltage-dependent, alpha 2/delta subunit 1       32206_at   up   0.000172847   CDC42 binding protein kinase alpha (DMPK-like)       39428_at   down   0.000182565   lymphocyte adaptor protein       41026_f_at   up   0.000185284   glycophorin B (includes Ss blood group)       37388_at   up   0.000226625   tissue factor pathway inhibitor 2       38691_s_at   up   0.000249289   surfactant, pulmonary-associated protein C       31700_at   up   0.000257409   G protein-coupled receptor 35       40107_at   up   0.000263914   aldolase C, fructose-bisphosphate       35541_r_at   up   0.000282816   KIAA0506 protein       36441_at   up   0.000286506       33177_at   up   0.000290145   hypothetical protein MGC4293       1836_at   down   0.000307175   cyclin I       37059_at   up   0.000311251   glucokinase (hexokinase 4) regulatory protein       34178_at   up   0.000352425   zinc finger protein 297       37631_at   up   0.000379094   myosin IE       34011_at   up   0.000383332   harakiri, BCL2 interacting protein (contains only BH3 domain)       31924_at   up   0.000406589   testicular soluble adenylyl cyclase       40354_at   up   0.000434143   heat shock protein (hsp110 family)       39016_r_at   up   0.00044483   keratin 6A       34213_at   up   0.000460936   KIBRA protein       480_at   up   0.000466565   membrane-associated tyrosine- and threonine-specific cdc2-                   inhibitory kinase       35952_at   up   0.00048402       33727_r_at   up   0.000532272   tumor necrosis factor receptor superfamily, member 6b, decoy       32671_at   up   0.000563318   KIAA0173 gene product       41714_at   up   0.000580592   KIAA0455 gene product       36000_at   up   0.000583128   cAMP responsive element binding protein-like 1       37473_at   up   0.000586685   keratin 16 (focal non-epidermolytic palmoplantar keratoderma)       934_at   up   0.00059989   glycosylphosphatidylinositol specific phospholipase D1       35996_at   up   0.00060253   ZW10 interactor anti-sense       38007_at   up   0.000616603   neurofibromin 2 (bilateral acoustic neuroma)       1187_at   up   0.000619655   ligase III, DNA, ATP-dependent       32701_at   up   0.000630146   armadillo repeat gene deletes in velocardiofacial syndrome       33960_s_at   up   0.00065576   calcium channel, voltage-dependent, L type, alpha 1B subunit       37584_at   up   0.000662109   Fanconi anemia, complementation group G       37551_at   up   0.000674595   KIAA0211 gene product       1937_at   up   0.00067796       33277_at   up   0.000693507   myotubularin related protein 2       36237_at   up   0.000693967   solute carrier family 22 (organic anion transporter), member 6       41377_f_at   up   0.000700545   UDP glycosyltransferase 2 family, polypeptide B7       35858_at   up   0.000706501   postmeiotic segregation increased 2-like 9       31495_at   up   0.000713236   chemokine (C motif) ligand 2       37413_at   up   0.000724544   dipeptidase 1 (renal)       36222_at   up   0.000729569   lymphocyte antigen 6 complex, locus G6C       39279_at   down   0.000742449   bone morphogenetic protein 6       37658_at   up   0.000769593   growth arrest-specific 6       34209_at   up   0.000774852   inositol 1,4,5-trisphosphate 3-kinase C       34963_at   up   0.000798158   collagen, type XIV, alpha 1 (undulin)       41081_at   up   0.00080125   BUB1 budding uninhibited by benzimidazoles 1 homolog (yeast)       40997_at   up   0.000802266   mitogen-activated protein kinase kinase kinase 12       35384_at   up   0.000812766   histamine receptor H1       268_at   down   0.000882562   platelet/endothelial cell adhesion molecule (CD31 antigen)       35890_at   up   0.000883719   sema domain, immunoglobulin domain (Ig), short basic domain,                   secreted, (semaphorin) 3D       33778_at   up   0.000883921   chromosome 22 open reading frame 4       258_at   up   0.000904043   lymphotoxin alpha (TNF superfamily, member 1)       35219_at   up   0.000908143   hypothetical protein MGC3047       35176_at   up   0.000955593   dolichyl-phosphate (UDP-N-acetylglucosamine) N-                   acetylglucosaminephosphotransferase 1                   (GlcNAc-1-P transferase)       32162_r_at   up   0.000971421       31391_at   up   0.001022205   huntingtin-associated protein 1 (neuroan 1)       34479_at   up   0.001039336   phosphoinositide-3-kinase, regulatory subunit, polypeptide 3                   (p55, gamma)       738_at   down   0.001062791   5′-nucleotidase, cytosolic II       35719_at   down   0.001077778   pleckstrin homology domain containing, family E                   (with leucine rich repeats) member 1       236_at   up   0.001119267   guanine nucleotide binding protein (G protein), alpha activating                   activity polypeptide O       33779_at   up   0.001119359   vesicle-associated membrane protein 1 (synaptobrevin 1)       31653_at   up   0.001120702   peter pan homolog ( Drosophila )       41644_at   up   0.001148448   KIAA0790 protein       35312_at   up   0.001149439   MCM2 minichromosome maintenance deficient 2, mitotin ( S. cerevisiae )       38202_at   up   0.001170423   FAT tumor suppressor homolog 2 ( Drosophila )       1943_at   up   0.001242703   cyclin A2       34894_r_at   up   0.001244784   protease, serine, 22       38162_at   up   0.001251007   regulating synaptic membrane exocytosis 2       689_at   up   0.001251663   paraneoplastic antigen       41694_at   up   0.001259985   polymerase (RNA) III (DNA directed) polypeptide D, 44 kDa       31991_at   up   0.0012619       41507_at   up   0.001276543   mitogen-activated protein kinase-activated protein kinase 5       34949_at   up   0.001318033   adaptor-associated kinase 1       33517_f_at   up   0.001327311   melanoma antigen, family A, 3       41483_s_at   down   0.001346791   jun D proto-oncogene       41641_at   up   0.001347939   GPI-anchored metastasis-associated protein homolog       35313_at   down   0.001365937   KIAA0310 gene product       37779_at   up   0.001386546   acid sphingomyelinase-like phosphodiesterase       388 _at   up   0.001392133   loricrin       1499_at   down   0.001398505   farnesyltransferase, CAAX box, alpha       35197_at   up   0.001406638       35853_at   up   0.001414183   protein kinase C, alpha binding protein       35932_at   up   0.001424663   left-right determination, factor B       39568_g_at   up   0.001432152   aquaporin 7       32000_g_at   up   0.001434142   ATP-binding cassette, sub-family A (ABC1), member 1       37436_at   up   0.001447929   mitochondrial capsule selenoprotein       34235_at   up   0.001481689   G protein-coupled receptor 116       36907_at   up   0.001501258   mevalonate kinase (mevalonic aciduria)       31882_at   up   0.001503925   RNA, U3 small nucleolar interacting protein 2       36535_at   down   0.001515459   microfibrillar-associated protein 1       1196_at   up   0.001528997   chromosome condensation 1       35505_at   up   0.00152955   SWI/SNF related, matrix associated, actin dependent                   regulator of chromatin, subfamily f, member 1       41118_at   up   0.001529915   hypothetical protein FLJ13639       34770_at   down   0.001530656   mitogen-activated protein kinase kinase kinase 8       37525_at   up   0.001547367   serine protease inhibitor-like, with Kunitz and WAP domains 1                   (eppin)       1285_at   up   0.001552251       643_at   up   0.001552712   nuclear receptor subfamily 0, group B, member 2       33031_at   up   0.001558992       37415_at   up   0.001572633   ATPase, Class V, type 10B       38353_at   down   0.001599369   tubulin, gamma complex associated protein 3       32106_at   up   0.001599378   serine (or cysteine) proteinase inhibitor, clade A (alpha-1                   antiproteinase, antitrypsin), member 4       31726_at   up   0.001621904   gamma-aminobutyric acid (GABA) A receptor, alpha 3       38027_at   up   0.001641281   fibulin 1       32420_at   up   0.001677644   G protein-coupled receptor 6       33854_at   down   0.00173595   ATPase, H+ transporting, lysosomal 34 kDa, V1 subunit D       39101_at   up   0.001763484   myosin, heavy polypeptide 2, skeletal muscle, adult       41502_at   up   0.001776846   homeodomain interacting protein kinase 3       39354_at   down   0.001786265   peroxiredoxin 6       39862_at   up   0.00179467   KIAA0296 gene product       38982_at   down   0.001798352   telomeric repeat binding factor 2, interacting protein       33640_at   up   0.001802226   allograft inflammatory factor 1       34131_at   up   0.001817414   solute carrier family 7, (cationic amino acid transporter,                   y+ system) member 11       31686_at   up   0.001831044   tubulin, beta polypeptide 4, member Q       33648_at   up   0.001850125       35035_at   up   0.001852417   cholinergic receptor, nicotinic, beta polypeptide 3       39570_at   up   0.001878741   hypothetical protein DKFZp434G2311       38125_at   up   0.001882819   serine (or cysteine) proteinase inhibitor, clade E (nexin,                   plasminogen activator inhibitor type 1), member 1       37978_at   up   0.001896075   quinolinate phosphoribosyltransferase (nicotinate-nucleotide                   pyrophosphorylase (carboxylating))       32010_at   up   0.001904026   hypothetical protein EAN57       39609_at   up   0.00193915   single-minded homolog 2 ( Drosophila )       39622_at   up   0.001950092   glial cells missing homolog 1 ( Drosophila )       38707_r_at   up   0.001970767   E2F transcription factor 4, p107/p130-binding       39520_at   up   0.001987141   KIAA0692 protein       34506_at   up   0.001990895   aminolevulinate, delta-, dehydratase       41771_g_at   up   0.001997028   monoamine oxidase A       36281_at   up   0.002006192   nescient helix loop helix 1       39899_at   up   0.002018086   TSLC1-like 2       262_at   down   0.002038292   adenosylmethionine decarboxylase 1       33281_at   up   0.002042034   inhibitor of kappa light polypeptide gene enhancer in B-cells,                   kinase epsilon       36730_at   up   0.002098173   ATP-binding cassette, sub-family C (CFTR/MRP), member 10       40236_at   up   0.002111687   solute carrier family 7 (cationic amino acid transporter,                   y+ system), member 2       36731_g_at   up   0.002115082   ATP-binding cassette, sub-family C (CFTR/MRP), member 10       282_at   up   0.002123585   M-phase phosphoprotein 1       41647_at   up   0.002129848   STE20-like kinase       33080_s_at   up   0.002156909   RAP1, GTPase activating protein 1       558_at   up   0.002159946   keratin 1 (epidermolytic hyperkeratosis)       39714_at   down   0.002160768   SH3 domain binding glutamic acid-rich protein like       34630_s_at   up   0.002160768   dynein, axonemal, heavy polypeptide 9       41200_at   up   0.002177956   scavenger receptor class B, member 1       40020_at   up   0.002182404   cadherin, EGF LAG seven-pass G-type receptor 3 (flamingo                   homolog,  Drosophila )       37953_s_at   up   0.002214218   amiloride-sensitive cation channel 2, neuronal       34425_at   up   0.002221153   major histocompatibility complex, class I-related       40957_at   down   0.002223327   joined to JAZF1       2046_at   up   0.002238232       31628_at   up   0.00224761   solute carrier family 15 (oligopeptide transporter), member 1       34590_at   up   0.002247733   ciliary neurotrophic factor       40219_at   up   0.002257582   HMBA-inducible       35502_at   up   0.00228274   anti-Mullerian hormone receptor, type II       32640_at   up   0.00229347   intercellular adhesion molecule 1 (CD54), human rhinovirus                   receptor       31596_f_at   up   0.0023025   immunoglobulin lambda-like polypeptide 2       35920_at   up   0.00234203   hemoglobin, beta pseudogene 1       41013_at   up   0.002357083       36084_at   up   0.00236503   KIAA0076 gene product       38171_at   up   0.00238626   WD-repeat protein       41209_at   up   0.002391825   lipoprotein lipase       38858_at   up   0.002394103   potassium voltage-gated channel, subfamily H (eag-related),                   member 2       40399_r_at   up   0.002401232   mesenchyme homeo box 2 (growth arrest-specific homeo box)       32141_at   up   0.002413611   protein phosphatase 1E (PP2C domain containing)       1681_at   up   0.002427249   estrogen receptor 1       32681_at   up   0.002434539   solute carrier family 9 (sodium/hydrogen exchanger), isoform 1                   (antiporter, Na+/H+, amiloride sensitive)       39097_at   down   0.002438561   SON DNA binding protein       435_g_at   up   0.002444462   H1 histone family, member 0       40400_at   up   0.002448507   adenosine A1 receptor       34704_r_at   up   0.002448849   chorionic somatomammotropin hormone 2       1662_r_at   up   0.002482635       35448_at   up   0.002497094   peptidylprolyl isomerase (cyclophilin)-like 2       32498_at   up   0.002516445   glutamate receptor, metabotropic 2       34370_at   down   0.002528889   archain 1       396_f_at   up   0.002531111   erythropoietin receptor       1035_g_at   up   0.002533413   tissue inhibitor of metalloproteinase 3 (Sorsby fundus dystrophy,                   pseudoinflammatory)       38957_at   up   0.00254188   doublecortin and CaM kinase-like 1       35921_at   up   0.002559242   hemoglobin, beta pseudogene 1       873_at   up   0.002587161   homeo box A5       545_g_at   down   0.002588546   nuclear factor of kappa light polypeptide gene enhancer in                   B-cells 2 (p49/p100)       309_f_at   up   0.002594278   growth hormone 2       1442_at   up   0.002597237   estrogen receptor 2 (ER beta)       1814_at   down   0.002601426   transforming growth factor, beta receptor II (70/80 kDa)       37153_at   up   0.002626944   nephronophthisis 4       41807_at   down   0.002629111   sin3-associated polypeptide, 18 kDa       38513_at   up   0.00264673   processing of precursors 1       33403_at   down   0.002651277   DKFZP547E1010 protein       786_at   up   0.002669364   polymerase (DNA directed), alpha       31975_at   up   0.002694514       38495_s_at   up   0.00271851   fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase,                   Lewis blood group included)       714_at   up   0.002720175       38482_at   up   0.00272614   claudin 7       1967_f_at   up   0.002739683       39240_at   up   0.002744223   neurexin 1       37575_at   down   0.002760815       1063_s_at   up   0.0027749   TYRO3 protein tyrosine kinase       31590_g_at   up   0.002776136       37898_r_at   up   0.002781402   trefoil factor 3 (intestinal)       37983_at   up   0.002787601   angiotensin II receptor, type 1       37273_at   up   0.002809352       926_at   up   0.002825805   metallothionein 1G       34293_at   up   0.002829536   kinesin family member C3       33821_at   down   0.00283335   homolog of yeast long chain polyunsaturated fatty acid                   elongation enzyme 2       36840_at   up   0.002837181   hypothetical protein FLJ10737       31889_at   up   0.002846254   melan-A       37151_at   up   0.002860716       32201_at   up   0.002868158   Sjogren&#39;s syndrome nuclear autoantigen 1       414_at   up   0.002884861   homeo box D10       35520_at   up   0.002889864   claudin 9       39666_at   up   0.002894488   guanine nucleotide binding protein (G protein), gamma 4       38621_at   up   0.002895693   dimethylarginine dimethylaminohydrolase 2       970_r_at   up   0.002920493   ubiquitin specific protease 9, X chromosome (fat facets-like                     Drosophila )       41247_at   up   0.002926933       1022_f_at   up   0.002930839   interferon, alpha 14       41500_at   up   0.002932033   v-ski sarcoma viral oncogene homolog (avian)       34679_at   up   0.002938559   breakpoint cluster region       33942_s_at   up   0.002939961   syntaxin binding protein 1       33454_at   up   0.002954371   agrin       32048_at   up   0.002956969       39567_at   up   0.002960606   aquaporin 7       734_at   up   0.003021185       40473_at   down   0.003051481   serine/threonine kinase 24 (STE20 homolog, yeast)       160029_at   down   0.003081574   protein kinase C, beta 1       37097_at   up   0.003086294   solute carrier family 17 (sodium phosphate), member 1       32172_at   down   0.003088013   SMART/HDAC1 associated repressor protein       38604_at   up   0.003091956   neuropeptide Y       34621_at   up   0.003098553   keratin 2A (epidermal ichthyosis bullosa of Siemens)       32349_at   up   0.003130675   annexin A10       38928_r_at   up   0.003143861   tyrosinase (oculocutaneous albinism IA)       1988_at   up   0.003144002   platelet-derived growth factor receptor, alpha polypeptide       1494_f_at   up   0.003151857   cytochrome P450, family 2, subfamily A, polypeptide 6       32156_at   up   0.003158238   poliovirus receptor-related 2 (herpesvirus entry mediator B)       34440_at   up   0.00317265   DiGeorge syndrome critical region gene 9       37853_at   up   0.003195503   urocortin       39839_at   down   0.003202074   cold shock domain protein A       38747_at   up   0.003205975   CD34 antigen       40565_at   up   0.003225285   apolipoprotein E       31326_at   up   0.003229141       40668_s_at   up   0.003236501   CD6 antigen       32923_r_at   up   0.003262936   synapsin I       33972_r_at   up   0.003267304   deleted in azoospermia-like       2027_at   up   0.003272896   S100 calcium binding protein A2       38038_at   up   0.003272965   lumican       34820_at   up   0.003338528   pleiotrophin (heparin binding growth factor 8, neurite growth-                   promoting factor 1)       34197_at   up   0.003357164   phosphoinositide-3-kinase, regulatory subunit, polypeptide 2                   (p85 beta)       41427_at   up   0.003380281   wingless-type MMTV integration site family, member 11         _at   up   0.003400348   potassium voltage-gated channel, shaker-related subfamily,                   beta member 1       192_at   down   0.003400695   TAF7 RNA polymerase II, TATA box binding protein (TBP)-                   associated factor, 55 kDa       34821_at   down   0.003403862   chromosome 6 open reading frame 80       33712_at   up   0.003430688   sulfotransferase family 4A, member 1       37588_s_at   up   0.003433268   mitogen-activated protein kinase 8 interacting protein 2       37372_at   up   0.003438532   sphingomyelin phosphodiesterase 1, acid lysosomal (acid                   sphingomyelinase)       40372_at   up   0.003447837   pancreatic lipase-related protein 1       441_s_at   up   0.003458549   leukemia inhibitory factor (cholinergic differentiation factor)       1849_s_at   down   0.003460555   retinoblastoma binding protein 1       541_g_at   up   0.003461606   heat shock 27 kDa protein 2       32443_at   up   0.003463616   zinc finger protein 157 (HZF22)       121_at   up   0.003467949   paired box gene 8       41817_g_at   up   0.00349005   caspase recruitment domain family, member 10       39242_at   up   0.003510672   synaptotagmin V       37687_i_at   up   0.003516194   Fc fragment of IgG, low affinity IIa, receptor for (CD32)       40302_at   up   0.003521173   emilin and multimerin-domain containing protein 1       39192_at   up   0.003526575   tumor necrosis factor receptor superfamily, member 17       39722_at   up   0.003536214   nuclear receptor co-repressor 1       31936_s_at   down   0.003552058   limkain b1       32407_f_at   up   0.003585808       36304_at   up   0.00359153   complement component 8, beta polypeptide       37270_at   up   0.003593677   ATPase, Na+/K+ transporting, beta 2 polypeptide       40171_at   down   0.003618084   frequently rearranged in advanced T-cell lymphomas 2       39495_at   up   0.003639204   hypothetical protein FLJ20719       37139_at   up   0.003644433   ectodermal dysplasia 1, anhidrotic       31681_at   up   0.003648646   erythropoietin receptor       41276_at   up   0.003680784   sin3-associated polypeptide, 18 kDa       36469_at   up   0.003682865   dystrobrevin, alpha       32810_at   up   0.003706452   thiopurine S-methyltransferase       34069_s_at   up   0.003710418   synovial sarcoma translocation, chromosome 18       37087_at   up   0.003723312   A kinase (PRKA) anchor protein 4       32513_at   up   0.003730609   neurofilament 3 (150 kDa medium)       614_at   up   0.003737015   phospholipase A2, group IIA (platelets, synovial fluid)       1019_g_at   up   0.003737542   wingless-type MMTV integration site family, member 10B       36123_at   down   0.003760113   thiosulfate sulfurtransferase (rhodanese)       33211_at   up   0.003774765   ribosome binding protein 1 homolog 180 kDa (dog)       38541_at   up   0.003778747   cytochrome P450, family 21, subfamily A, polypeptide 2       39343_at   up   0.003780079   transformer-2 alpha (htra-2 alpha)       36888_at   up   0.00379196   KIAA0841 protein       37312_at   down   0.003803597   transcriptional regulator interacting with the PHS-bromodomain 2       37785_at   up   0.003817423   GTP-binding protein       33323_r_at   up   0.003818801   stratifin       35633_at   down   0.003823077   engulfment and cell motility 1 (ced-12 homolog,  C. elegans )       34273_at   up   0.003831402   regulator of G-protein signalling 4       35545_at   up   0.003835274   solute carrier family 4, sodium bicarbonate cotransporter,                   member 8       33661_at   up   0.003844513   ribosomal protein L5       40359_at   up   0.003849677   chromosome 11 open reading frame 13       37056_at   up   0.003860515   tec protein tyrosine kinase       33268_at   up   0.003860581   Smcx homolog, X chromosome (mouse)       37618_at   up   0.003865292   homeo box B7       36323_at   up   0.003868425   gamma-aminobutyric acid (GABA) A receptor, alpha 1       31654_at   up   0.003872787   VPS10 domain receptor protein SORCS 3       39990_at   up   0.003883048   ISL1 transcription factor, LIM/homeodomain, (islet-1)       38608_at   up   0.003891136   lectin, galactoside-binding, soluble, 7 (galectin 7)       35746_r_at   down   0.003899767   poly(rC) binding protein 2       259_s_at   up   0.003922965   tumor necrosis factor (TNF superfamily, member 2)       34558_at   up   0.00393898   opiate receptor-like 1       34457_at   up   0.003943871   solute carrier family 30 (zinc transporter), member 3       31771_at   up   0.003954233       32292_at   up   0.003968658   collectin sub-family member 10 (C-type lectin)       32171_at   down   0.003976408   eukaryotic translation initiation factor 5       37166_at   up   0.004008678   3-hydroxyanthranilate 3,4-dioxygenase       1612_s_at   down   0.004008843   jun D proto-oncogene       38636_at   up   0.004009285   immunoglobulin superfamily containing leucine-rich repeat       39939_at   up   0.004024305   collagen, type IV, alpha 6       39459_at   up   0.004034943   ribosomal protein S13       41437_at   down   0.004042248   chromosome 14 open reading frame 109       872_i_at   up   0.00408932   insulin receptor substrate 1       39091_at   down   0.004093417   vitamin A responsive; cytoskeleton related       35319_at   down   0.004100726   CCCTC-binding factor (zinc finger protein)       33967_at   up   0.004109676   major histocompatibility complex, class II, DO alpha       333_s_at   down   0.004110914       39400_at   up   0.00412939   KIAA1055 protein       39304_g_at   up   0.004129597   beta-transducin repeat containing       37838_at   up   0.004143313   coagulation factor XII (Hageman factor)       35970_g_at   down   0.00414378   M-phase phosphoprotein 9       1669_at   up   0.004147458   wingless-type MMTV integration site family, member 5A       38822_at   up   0.004163563   serine/threonine kinase 17a (apoptosis-inducing)       145_s_at   up   0.004167288   T-box 5       38883_at   up   0.004187484       39917_at   up   0.004214466   tubulin, gamma complex associated protein 2       32650_at   up   0.004216408   neuronal protein       35007_at   down   0.004227977       41655_at   up   0.004234936   midline 2       37731_at   down   0.004243561   epidermal growth factor receptor pathway substrate 15       34066_at   up   0.004275892   hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)       33885_at   down   0.004286872   KIAA0907 protein       37025_at   down   0.004312041   lipopolysaccharide-induced TNF factor       35699_at   up   0.004318144   BUB1 budding uninhibited by benzimidazoles 1 homolog beta                   (yeast)       36129_at   up   0.004340344   KIAA0397 gene product       32629_f_at   up   0.004351049   butyrophilin, subfamily 3, member A1       40625_f_at   up   0.004352482   metaxin 1       37465_at   up   0.004357604   brain-specific protein p25 alpha       1700_at   up   0.00436827   BCL2 binding component 3       32345_at   up   0.00437274       35281_at   up   0.004383388   laminin, gamma 2       32358_at   up   0.004391543   WNT1 inducible signaling pathway protein 3       32007_at   up   0.004446678       35803_at   up   0.004448806   ras homolog gene family, member E       35630_at   up   0.004449475   lethal giant larvae homolog 2 ( Drosophila )       33467_at   up   0.004454387   CMRF35 leukocyte immunoglobulin-like receptor       41449_at   up   0.004456743   sarcoglycan, epsilon       1075_f_at   up   0.004457857   interferon, alpha 16       1567_at   up   0.004477979   fms-related tyrosine kinase 1 (vascular endothelial growth                   factor/vascular permeability factor receptor)       32223_at   up   0.004484703   splicing factor, arginine/serine-rich 14       35745_f_at   down   0.004489339   poly(rC) binding protein 2       32888_at   up   0.00451066   leukocyte tyrosine kinase       1777_at   up   0.004521209   Ras and Rab interactor 1       40042_r_at   up   0.004524196   proline dehydrogenase (oxidase) 1       35896_at   up   0.004592292   DKFZp434P211 protein       34702_f_at   up   0.004610914   chorionic somatomammotropin hormone 2       1339_s_at   up   0.004621845   breakpoint cluster region       1799_at   up   0.004625646   excision repair cross-complementing rodent repair deficiency,                   complementation group 4       35320_at   up   0.004625842   solute carrier family 11 (proton-coupled divalent metal ion                   transporters), member 2       37191_at   up   0.00462609   phytanoyl-CoA hydroxylase interacting protein       33521_at   up   0.004640954   ATPase, H+/K+ exchanging, alpha polypeptide       34527_r_at   up   0.004649009       34467_g_at   up   0.004656371   5-hydroxytryptamine (serotonin) receptor 4       37760_at   up   0.004663199   BAI1-associated protein 2       33418_at   down   0.004726336       39720_g_at   up   0.00473358   zona pellucida glycoprotein 3 (sperm receptor)       32028_at   up   0.004738157   phosphomannomutase 2       35666_at   up   0.004741066   sema domain, immunoglobulin domain (Ig), short basic domain,                   secreted, (semaphorin) 3F       31591_s_at   up   0.004769075   complement factor H-related 4       39009_at   down   0.004782089   LSM3 homolog, U6 small nuclear RNA associated ( S. cerevisiae )       38847_at   up   0.004785318   maternal embryonic leucine zipper kinase       37793_r_at   up   0.004797672   RAD51-like 3 ( S. cerevisiae )       32837_at   up   0.004799361   1-acylglycerol-3-phosphate O-acyltransferase 2                   (lysophosphatidic acid acyltransferase, beta)       32092_at   up   0.004804199   syndecan 3 (N-syndecan)       35307_at   down   0.004819968   GDP dissociation inhibitor 2       34141_at   up   0.004824997       40321_at   up   0.004840659   interleukin 1 receptor-like 1       40622_r_at   up   0.004881409   ubiquitin protein ligase       39128_r_at   up   0.004896276   protein phosphatase 2A, regulatory subunit B′ (PR 53)       36819_at   up   0.004902066   Machado-Joseph disease (spinocerebellar ataxia 3,                   olivopontocerebellar ataxia 3, autosomal dominant, ataxin 3)       36702_at   up   0.004916649   T-box 19       1828_s_at   up   0.004940536   fibroblast growth factor 2 (basic)       33047_at   up   0.004989688       41192_at   down   0.004996772   hypothetical protein 669       33134_at   up   0.005003649   adenylate cyclase 3       564_at   up   0.005026874   guanine nucleotide binding protein (G protein), alpha 11 (Gq                   class)       38797_at   up   0.005038875   KIAA0062 protein       40276_at   down   0.005046073   proteasome (prosome, macropain) 26S subunit, non-                   ATPase, 7 (Mov34 homolog)       40199_at   up   0.005054057   msh homeo box homolog 1 ( Drosophila )       31818_at   up   0.005058057       1832_at   up   0.00506241   mutated in colorectal cancers       39051_at   up   0.005064802   neuronatin       31676_at   up   0.005081672   zinc finger protein 208       32479_at   up   0.005105492   tumor necrosis factor receptor superfamily, member 11a,                   activator of NFKB       39197_s_at   up   0.005111726       39750_at   up   0.005142581   zinc finger, DHHC domain containing 3       39986_at   up   0.005154791   hepatocellularcarcinoma-associated antigen HCA557a       37053_at   up   0.005195125   ATPase, Ca++ transporting, plasma membrane 2       32389_at   up   0.005199094   RNA, U2 small nuclear       40376_at   up   0.005209375   arylsulfatase E (chondrodysplasia punctata 1)       1379_at   up   0.005219489   EphA2       38440_s_at   down   0.005255831   hypothetical protein FLJ20811       33520_at   up   0.005264186   coagulation factor VII (serum prothrombin conversion                   accelerator)       39688_at   up   0.00527689   requiem, apoptosis response zinc finger gene       31829_r_at   up   0.005284494   trans-golgi network protein 2       2066_at   up   0.005318536   BCL2-associated X protein       38294_at   up   0.005318622   homeo box D4       32971_at   up   0.00533295   Friedreich ataxia region gene X123       32509_at   up   0.005359441   HBxAg transactivated protein 2       41227_at   up   0.00537468   oculocerebrorenal syndrome of Lowe       41840_r_at   up   0.005385137       1804_at   up   0.005407113   kallikrein 3, (prostate specific antigen)       34703_f_at   up   0.005425622   chorionic somatomammotropin hormone 2       34060_g_at   up   0.005447522   Pvt1 oncogene homolog, MYC activator (mouse)       39499_s_at   up   0.005466238   par-3 partitioning defective 3 homolog ( C. elegans )       32240_at   up   0.005479107   proteasome (prosome, macropain) 26S subunit, non-ATPase, 5       31817_at   up   0.005494234   gamma-aminobutyric acid (GABA) A receptor, beta 3       32077_s_at   up   0.005543575   potassium voltage-gated channel, KQT-like subfamily, member 1       33762_r_at   up   0.005564914   KIAA0493 protein       37459_at   up   0.005565205   collagen, type VIII, alpha 1       1240_at   up   0.00556878   caspase 2, apoptosis-related cysteine protease (neural precursor                   cell expressed, developmentally down-regulated 2)       33711_at   up   0.00557075   prooplomelanocortin (adrenocorticotropin/beta-lipotropin/alpha-                   melanocyte stimulating hormone/beta-melanocyte stimulating                   hormone/beta-endorphin)       31411_at   up   0.005579666   variable charge, Y chromosome, 2       36337_at   up   0.005593633   KIAA0963 protein       40340_at   up   0.005596156   hypothetical protein DKFZp586E1923       35536_at   up   0.005620504   endothelin converting enzyme 2       33000_at   up   0.005629213   hepatitis A virus cellular receptor 1       34906_g_at   up   0.005635263   glutamate receptor, ionotropic, kainate 5       37721_at   up   0.005646504   deoxyhypusine synthase       32642_at   up   0.005651069   chondroitin sulfate proteoglycan 3 (neurocan)       39160_at   down   0.005660176   pyruvate dehydrogenase (lipoamide) beta       41264_at   up   0.005670964       34655_at   up   0.0057165   membrane protein, palmitoylated 2 (MAGUK p55 subfamily                   member 2)       31861_at   up   0.005718235   immunoglobulin mu binding protein 2       36734_at   up   0.005753457   small proline-rich protein 2A       39310_at   up   0.005754564   bradykinin receptor B2       770_at   up   0.005756245   glutathione peroxidase 3 (plasma)       764_s_at   up   0.005789206   clock homolog (mouse)       31350_at   up   0.005792228   olfactory receptor, family 10, subfamily H, member 3       40615_at   down   0.005797033   hypothetical protein FLJ21439       38180_f_at   up   0.005826003   pregnancy specific beta-1-glycoprotein 9       33574_at   up   0.005842528   chromosome 6 open reading frame 10       33986_r_at   up   0.005846995   heat shock 90 kDa protein 1, beta       31542_at   up   0.005886628   filaggrin       36578_at   down   0.005897302   baculoviral IAP repeat-containing 2       31442_at   up   0.005902455       37839_at   up   0.005906266       39445_at   up   0.005922975   UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 3       41046_s_at   up   0.00592598   zinc finger protein 261       36546_r_at   up   0.005940762   KIAA0542 gene product       40907_at   up   0.005948234   hypothetical protein FLJ32130       160020_at   up   0.005967887   matrix metalloproteinase 14 (membrane-inserted)       41793_at   up   0.005969246   ATP-binding cassette, sub-family C (CFTR/MRP), member 8       35899_at   up   0.00598163   artemin       41354_at   up   0.005996623   stanniocalcin 1       731_f_at   up   0.006023842       41051_at   down   0.006083685   translin-associated factor X       39598_at   up   0.006099426   gap junction protein, beta 1, 32 kDa (connexin 32, Charcot-Marie-                   Tooth neuropathy, X-linked)       40877_s_at   up   0.006100957   D15F37 (pseudogene)       39619_at   up   0.006107927   SGC32445 protein       40554_at   up   0.006116743   golgi phosphoprotein 4       548_s_at   down   0.006131531   spleen tyrosine kinase       230_s_at   up   0.00614997   follicle stimulating hormone, beta polypeptide       35637_at   up   0.006154739   hypothetical protein PRO2325       32241_at   down   0.006160593   TAR DNA binding protein       2077_at   up   0.006189769   integrin, alpha 6       40825_at   up   0.00622426   microtubule-associated protein, RP/EB family, member 3       39472_s_at   up   0.006239579   BRAF35/HDAC2 complex (80 kDa)       38320_s_at   up   0.006246922   lipase, hormone-sensitive       37972_at   up   0.006252496   deoxyribonuclease I-like 3       31410_at   up   0.006253494   tumor necrosis factor receptor superfamily, member 13B       33594_at   up   0.006264788   dickkopf homolog 4 (Xenopus laevis)       40081_at   up   0.00627529   phospholipid transfer protein       34301_r_at   up   0.006279415   keratin 17       35329_at   down   0.006296693   cytochrome b5 reductase 1 (B5R.1)       31709_at   up   0.006341656   nuclear receptor co-repressor 2       34415_at   up   0.006342999   activin A receptor, type IB       31406_at   up   0.006344356   G protein-coupled receptor 50       35254_at   up   0.006348896   FLN29 gene product       31930_f_at   up   0.006378393   Rhesus blood group, CcEe antigens       38460_at   up   0.006382402   cytochrome b-5       31537_at   up   0.006385628   ADP-ribosyltransferase 1       33538_at   up   0.006387439   myelin expression factor 2       916_at   up   0.006393536   protein tyrosine phosphatase, receptor type, N       35599_at   up   0.006406575   glycine N-methyltransferase       35950_at   up   0.006461703   synovial sarcoma, X breakpoint 4       38468_at   up   0.006474053   Hermansky-Pudlak syndrome 1       1792_g_at   up   0.006476549   cyclin-dependent kinase 2       33064_at   up   0.006495075   calcium channel, voltage-dependent, gamma subunit 1       1680_at   up   0.006503388   growth factor receptor-bound protein 7       34429_at   up   0.006513609   mucosal vascular addressin cell adhesion molecule 1       36600_at   down   0.006518042   proteasome (prosome, macropain) activator subunit 1 (PA28                   alpha)       34108_g_at   up   0.006518826   6-phosphofructo-2-kinase/fructose-2,6 biphosphatase 2       36727_at   up   0.006526838       732_f_at   up   0.006547759       31668_f_at   up   0.006549214   erythrocyte membrane protein band 4.1-like 2       33784_at   up   0.006564337   TNF receptor-associated factor 2       40570_at   down   0.006567141   forkhead box O1A (rhabdomyosarcoma)       34853_at   up   0.006610556   fibronectin leucine rich transmembrane protein 2       571_at   down   0.006623427   nucleosome assembly protein 1-like 1       33532_at   up   0.006633032   cartilage paired-class homeoprotein 1       38597_f_at   up   0.00663979   solute carrier family 11 (proton-coupled divalent metal ion                   transporters), member 1       31534_at   up   0.006657321   zinc finger protein, Y-linked       35248_at   up   0.006666707   solute carrier family 19 (thiamine transporter), member 2       35938_at   down   0.006675236   phospholipase A2, group IVA (cytosolic, calcium-dependent)       32430_at   up   0.006677844   gastrin-releasing peptide receptor       35923_at   up   0.006705555   cholecystokinin B receptor       40145_at   up   0.006774519   topoisomerase (DNA) II alpha 170 kDa       35013_at   up   0.006804943   lipopolysaccharide binding protein       35898_at   up   0.00681255   WNT1 inducible signaling pathway protein 2       41331_at   up   0.006837963   leucine-rich repeats and immunoglobulin-like domains 2       34308_at   down   0.006842048   histone 1, H2ac       34795_at   up   0.006845198   procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine                   hydroxylase) 2       38205_at   up   0.006846391   neurogenic differentiation 2       739_at   up   0.006849272   neurofibromin 1 (neurofibromatosis, von Recklinghausen disease,                   Watson disease)       1208_at   up   0.006860724   PTK6 protein tyrosine kinase 6       38237_at   up   0.006873965   gamma-glutamyltransferase-like activity 1       37061_at   up   0.006878942   chitinase 1 (chitotriosidase)       31897_at   up   0.006912079   downregulated in ovarian cancer 1       34259_at   up   0.006921783   KIAA0664 protein       33510_s_at   up   0.006943429   glutamate receptor, metabotropic 1       37547_at   up   0.006943934   PTH-responsive osteosarcoma B1 protein       38032_at   up   0.006964957   synaptic vesicle glycoprotein 2A       41799_at   up   0.006993973   DnaJ (Hsp40) homolog, subfamily C, member 7       775_at   up   0.00699531   5-hydroxytryptamine (serotonin) receptor 1B       34175_r_at   up   0.00700068       36833_at   down   0.007015057   galactosidase, alpha       34405_at   up   0.007020147   ubiquitin specific protease 5 (isopeptidase T)       31745_at   up   0.007034964   mucin 3A, intestinal       38507_at   up   0.007046638   cytochrome P450, family 2, subfamily D, polypeptide 6       38504_at   up   0.00705255   calpain 5       31921_at   up   0.007070315   olfactory receptor, family 2, subfamily F, member 1       715_s_at   up   0.007073157   gamma-glutamyltransferase 1       214_at   up   0.007077911   msh homeo box homolog 1 ( Drosophila )       41833_at   up   0.007130788   jumping translocation breakpoint       36883_at   up   0.007136738   keratin 13       36404_at   up   0.007145174   glucagon-like peptide 1 receptor       799_at   up   0.007165141   cyclin-dependent kinase 5, regulatory subunit 1 (p35)       39805_at   up   0.00717185   ATP-binding cassette, sub-family B (MDR/TAP), member 6       38136_at   up   0.007176078   Werner syndrome       38193_at   up   0.007185711   immunoglobulin kappa constant       37939_at   up   0.007225072   apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like                   3C       265_s_at   up   0.00723378   selectin E (endothelial adhesion molecule 1)       39196_i_at   up   0.007240769   leucine-rich repeats and immunoglobulin-like domains 1       37129_at   up   0.007242263   neuropeptide FF-amide peptide precursor       35243_at   up   0.007262299   PCTAIRE protein kinase 3       34167_s_at   up   0.007272108   solute carrier family 6 (neurotransmitter transporter, L-proline),                   member 7       40523_at   up   0.007280257   forkhead box A2       1925_at   up   0.007284827   cyclin F       41340_at   up   0.00729114   sema domain, immunoglobulin domain (Ig), and GPI membrane                   anchor, (semaphorin) 7A       911_s_at   down   0.007294306   calmodulin 2 (phosphorylase kinase, delta)       1463_at   down   0.007297165   protein tyrosine phosphatase, non-receptor type 12       35816_at   down   0.007313124   cystatin B (stefin B)       34061_at   up   0.00731512   Pvt1 oncogene homolog, MYC activator (mouse)       363_at   up   0.007332831   protein kinase C, gamma       AFFX-BioC-3_at   up   0.007343487       37638_at   up   0.007365403   dedicator of cyto-kinesis 1       37778_at   down   0.007365593   KIN, antigenic determinant of recA protein homolog (mouse)       36252_at   up   0.007369173   cardiotrophin 1       33568_at   up   0.007372628   cholinergic receptor, nicotinic, beta polypeptide 4       37432_g_at   up   0.007374815   Msx-interacting-zinc finger       35317_at   down   0.007374906   meningioma expressed antigen 5 (hyaluronidase)       1100_at   down   0.007398264   interleukin-1 receptor-associated kinase 1       31841_at   up   0.007402655   catenin (cadherin-associated protein), alpha 2       34754_at   up   0.007404094   ezrin-binding partner PACE-1       921_s_at   up   0.007411006       39099_at   down   0.007442413   Sec23 homolog A ( S. cerevisiae )       32998_at   up   0.007466948   cholecystokinin A receptor       34752_at   down   0.007502681   NIMA (never in mitosis gene a)-related kinase 7       37906_at   up   0.007506317   latent transforming growth factor beta binding protein 2       32305_at   up   0.007531192   collagen, type I, alpha 2       32222_at   up   0.007545106   hypothetical protein FLJ14639       33067_at   up   0.007558906   histone 1, H1a       34680_s_at   down   0.007566871   KIAA0107 gene product       602_s_at   up   0.00758131   hydroxysteroid (17-beta) dehydrogenase 1       34466_at   up   0.007587165   5-hydroxytryptamine (serotonin) receptor 4       36790_at   down   0.007671431   tropomyosin 1 (alpha)       35000_at   up   0.007695054   tumor necrosis factor (ligand) superfamily, member 9       41619_at   up   0.007696786   interferon regulatory factor 6       33351_at   down   0.007707386   translation factor sui1 homolog       34406_at   up   0.007730668   KIAA0602 protein       118_at   up   0.007740152   inositol 1,4,5-trisphosphate 3-kinase A       34315_at   up   0.007744077   AFG3 ATPase family gene 3-like 2 (yeast)       39241_at   up   0.007758585   carbonic anhydrase I       1475_s_at   up   0.007800059   v-myb myeloblastosis viral oncogene homolog (avian)       39694_at   up   0.00783975   hypothetical protein MGC5508       272_at   up   0.007842252   gastrin-releasing peptide       1827_s_at   up   0.007852219   v-myc myelocytomatosis viral oncogene homolog (avian)       32592_at   up   0.007864197   KIAA0323 protein       40844_at   down   0.007876275   SH2 domain binding protein 1 (tetratricopeptide repeat containing)       35445_at   up   0.00787895   sorting nexin 26       35738_at   down   0.007881499   high mobility group nucleosomal binding domain 4       35306_at   down   0.007886283   DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 15       33016_at   up   0.007891585       34359_at   down   0.007895012   CGI-130 protein       37683_at   down   0.007902912   ubiquitin specific protease 10       40943_at   up   0.007973159   long-chain fatty-acyl elongase       882_at   up   0.007997396   colony stimulating factor 1 (macrophage)       40160_at   down   0.007999975   POM121 membrane glycoprotein (rat)       34845_at   up   0.008026503   CGI-51 protein       41076_at   up   0.008027637   gap junction protein, beta 3, 31 kDa (connexin 31)       40406_at   up   0.00804141   macrophage stimulating, pseudogene 9       34296_at   up   0.008078528   midline 1 (Opitz/BBB syndrome)       33866_at   down   0.008090063   tropomyosin 4       33493_at   up   0.008093623   erythroid differentiation and denucleation factor 1       37407_s_at   up   0.008123032   myosin, heavy polypeptide 11, smooth muscle       33707_at   up   0.008136505   phospholipase A2, group IVC (cytosolic, calcium-independent)       31609_s_at   up   0.00813732   procollagen C-endopeptidase enhancer       38991_at   up   0.008149715   KIAA0220 protein       34773_at   down   0.008173332   tubulin-specific chaperone a       39262_at   up   0.008173678   protein predicted by clone 23627       1116_at   up   0.008206557   CD19 antigen       863_g_at   up   0.008219712   serine (or cysteine) proteinase inhibitor, clade B (ovalbumin),                   member 5       35340_at   down   0.008224703   mel transforming oncogene (derived from cell line NK14)-RAB8                   homolog       34367_at   up   0.00822972   phosphoglycerate dehydrogenase       36585_at   down   0.008245871   ADP-ribosylation factor 4       33105_at   up   0.008266479   pleckstrin homology domain containing, family B (evectins)                   member 1       33169_at   up   0.008284475   neogenin homolog 1 (chicken)       40161_at   up   0.008318429   cartilage oligomeric matrix protein (pseudoachondroplasia,                   epiphyseal dysplasia 1, multiple)       38816_at   up   0.008319784   transforming, acidic coiled-coil containing protein 2       38687_at   down   0.008331445   DKFZP566D193 protein       34662_at   up   0.008344705   myc-induced nuclear antigen, 53 kDa       38400_at   down   0.008348744   DKFZP434D1335 protein       38052_at   down   0.008362106   coagulation factor XIII, A1 polypeptide       34556_at   up   0.008416122   keratin 9 (epidermolytic palmoplantar keratoderma)       39662_s_at   up   0.008428792   G protein-coupled receptor kinase 2-like ( Drosophila )       32188_at   up   0.008428989   myelin transcription factor 1       36684_at   down   0.008431467   adenosylmethionine decarboxylase 1       34436_at   up   0.008455809   solute carrier family 17 (sodium phosphate), member 3       38607_at   up   0.008486615   transmembrane 4 superfamily member 5       41428_at   up   0.008492173   ATP-binding cassette, sub-family C (CFTR/MRP), member 5       31923_f_at   up   0.008506636   ubiquilin 2       34365_at   up   0.008508922   peptidylprolyl isomerase E (cyclophilin E)       36242_at   up   0.008513005   small proline-rich protein 2C       38132_at   up   0.008552125   CDC42 effector protein (Rho GTPase binding) 1       1177_at   up   0.008558202       36706_at   up   0.008564806   cyclin-dependent kinase-like 5       41021_s_at   up   0.0085664   glycerol-3-phosphate dehydrogenase 2 (mitochondrial)       38067_at   up   0.008583304   likely ortholog of mouse septin 8       33740_at   up   0.00860968   chromosome 1 open reading frame 2       1167_s_at   up   0.008638816   matrix metalloproteinase 15 (membrane-inserted)       1726_at   up   0.008668644       40847_at   up   0.008669583   flavoprotein oxidoreductase MICAL2       37368_at   up   0.008705091   nuclear factor of activated T-cells, cytoplasmic, calcineurin-                   dependent 4       40277_at   up   0.008712834   golgi associated, gamma adaptin ear containing, ARF binding                   protein 2       35955_at   up   0.008714371   cytochrome c-like antigen       41233_at   down   0.008722182   DnaJ (Hsp40) homolog, subfamily B, member 6       40649_at   up   0.008763293   proprotein convertase subtilisin/kexin type 1       36338_at   up   0.008782835   leucine zipper protein 1       35194_at   up   0.008788982   glutathione peroxidase 2 (gastrointestinal)       40304_at   up   0.008813094   bullous pemphigoid antigen 1, 230/240 kDa       34559_at   up   0.008828164       34753_at   down   0.008836314   synaptobrevin-like 1       40834_at   up   0.008856926   PDZ domain containing 3       1025_g_at   up   0.008860423   cytochrome P450, family 1, subfamily A, polypeptide 1       31352_at   up   0.008862037       38050_at   down   0.008880693   Bcl-2-associated transcription factor       33072_at   up   0.008883812   hypocretin (orexin) receptor 2       41792_at   up   0.00888827   ATP-binding cassette, sub-family C (CFTR/MRP), member 8       35492_at   up   0.008900509   cytochrome P450, family 4, subfamily F, polypeptide 12       707_s_at   up   0.008954052       678_at   up   0.00896   alkaline phosphatase, placental-like 2       39633_at   up   0.008965521   S100 calcium binding protein A3       35379_at   up   0.008977482   collagen, type IX, alpha 1       38217_at   up   0.00898785   carboxyl ester lipase (bile salt-stimulated lipase)       33788_at   down   0.00901526   lysosomal apyrase-like 1       454_at   up   0.009032927   SWI/SNF related, matrix associated, actin dependent regulator of                   chromatin, subfamily d, member 1       466_at   down   0.00903801   general transcription factor II, i       1030_s_at   down   0.009041555   topoisomerase (DNA) I       39198_s_at   up   0.00906008   CGI-87 protein       40529_at   up   0.009060975   LIM homeobox protein 2       32098_at   up   0.009061067   collagen, type VI, alpha 2       37981_at   up   0.009065909   drebrin 1       36103_at   up   0.009068444   chemokine (C—C motif) ligand 3       40389_at   up   0.009068618   solute carrier family 38, member 3       40423_at   up   0.009110888   KIAA0903 protein       37885_at   up   0.009118294   hypothetical protein AF038169       39308_r_at   up   0.009130611   clathrin, light polypeptide (Lcb)       39468_r_at   up   0.009165844       34458_at   up   0.009174722   S100 calcium binding protein A7 (psoriasin 1)       39583_at   up   0.009175879   glioma amplified on chromosome 1 protein (leucine-rich)       34816_at   down   0.009179229   E1A binding protein p400       35275_at   up   0.009197426   adaptor-related protein complex 1, gamma 1 subunit       170_at   up   0.009214034   caudal type homeo box transcription factor 2       38059_g_at   up   0.009215265   dermatopontin       40501_s_at   up   0.00921917   myosin binding protein C, slow type       32372_at   up   0.00922417   cathepsin B       1957_s_at   up   0.009230348   transforming growth factor, beta receptor I (activin A receptor type                   II-like kinase, 53 kDa)       123_at   up   0.009235174   protein kinase C, mu       39150_at   down   0.009258766   ring finger protein 11       36813_at   up   0.009266999   thyroid hormone receptor interactor 13       38758_at   up   0.009277164   PDGFA associated protein 1       32198_at   up   0.009286085   hypothetical protein FLJ20452       39667_at   up   0.009305838   neuro-oncological ventral antigen 2       1796_s_at   up   0.009311292   B-cell CLL/lymphoma 3       35279_at   down   0.009332113   Tax1 (human T-cell leukemia virus type I) binding protein 1       32405_at   up   0.009349281   thioesterase, adipose associated       31785_f_at   up   0.009376814   unnamed HERV-H protein       41458_at   up   0.009388812   KIAA0467 protein       34443_at   up   0.009406186       31324_at   up   0.009411243       32303_at   up   0.00943436   ets variant gene 3       32915_at   up   0.00943445       37004_at   up   0.009438749   surfactant, pulmonary-associated protein B       35481_at   up   0.009450411   myosin heavy chain Myr 8       33282_at   up   0.009471432   ladinin 1       41307_at   up   0.009526397   CCR4-NOT transcription complex, subunit 2       39238_at   up   0.009533529   putative tumor suppressor       41114_at   up   0.009572837   microtubule associated testis specific serine/threonine protein                   kinase       39635_at   up   0.009598631   KIAA0960 protein       867_s_at   up   0.009646891   thrombospondin 1       1289_at   up   0.009657092   glutathione S-transferase M5       39132_at   down   0.009658304   SWI/SNF related, matrix associated, actin dependent regulator of                   chromatin, subfamily a, member 5       31980_at   up   0.009659298   winged-helix nude       33075_at   up   0.009675595   p21 (CDKN1A)-activated kinase 3       38448_at   up   0.009681742   actinin, alpha 2       34089_at   up   0.009695291   KIAA1030 protein       31587_at   up   0.009704155   solute carrier family 14 (urea transporter), member 2       31390_at   up   0.00970876   zinc finger protein 154 (pHZ-92)       31644_at   up   0.009719178   chemokine (C—C motif) ligand 27       1760_s_at   up   0.009726568   protein tyrosine phosphatase, non-receptor type 7       40491_at   up   0.009743005   retinoblastoma binding protein 1-like 1       36815_at   up   0.009778133       33969_at   up   0.009780589   interferon, omega 1       32784_at   down   0.009784866   PRP4 pre-mRNA processing factor 4 homolog B (yeast)       40861_at   down   0.009811631   mortality factor 4 like 2       39473_r_at   up   0.0099094   protein tyrosine phosphatase type IVA, member 3       40058_s_at   up   0.009913258   LIM protein (similar to rat protein kinase C-binding enigma)       1722_at   up   0.009928793   mitogen-activated protein kinase kinase 5       41074_at   up   0.009948477   G protein-coupled receptor 49       1488_at   up   0.009953543   protein tyrosine phosphatase, receptor type, K       38850_at   up   0.009961288       1746_s_at   up   0.009966628       39059_at   up   0.009967884   7-dehydrocholesterol reductase       40252_g_at   up   0.009972964   HIV-1 rev binding protein 2       35695_at   down   0.009979132   Chediak-Higashi syndrome 1       34952_at   up   0.010018587   Dombrock blood group       38734_at   up   0.010025605   phospholamban       36737_at   up   0.010027033   crystallin, beta A4       41025_r_at   up   0.010038866   glycophorin E       36020_at   up   0.010041904   KIAA1641 protein       39281_at   up   0.010049567   Rho guanine nucleotide exchange factor (GEF) 11       31931_f_at   up   0.010060411   Rhesus blood group, CcEe antigens       380_at   up   0.010096649   T-box 5       31471_at   up   0.010173071       32699_s_at   up   0.010181466   poliovirus receptor       36869_at   up   0.010188243   paired box gene 8       1241_at   down   0.010202166   protein tyrosine phosphatase type IVA, member 2       833_at   up   0.010217675   integrin, alpha X (antigen CD11C (p150), alpha polypeptide)       1296_at   up   0.01026762   cadherin 15, M-cadherin (myotubule)       40142_at   up   0.010274697   DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 24       41783_at   up   0.010279779   cellular retinoic acid binding protein 2       40294_at   up   0.010290318   ATP-binding cassette, sub-family B (MDR/TAP), member 9       38170_at   up   0.010301634       36398_at   up   0.010305459   RNA, U2 small nuclear       41127_at   up   0.010310422   solute carrier family 1 (glutamate/neutral amino acid transporter),                   member 4       41445_at   up   0.010315079   transforming growth factor, beta 1 (Camurati-Engelmann disease)       37184_at   up   0.010336804   syntaxin 1A (brain)       37515_at   up   0.010347685   mannan-binding lectin serine protease 2       39640_at   up   0.010360104   glutamine-fructose-6-phosphate transaminase 2       33823_at   up   0.010369528   scavenger receptor class B, member 2       34448_s_at   up   0.010370222   caspase 2, apoptosis-related cysteine protease (neural precursor                   cell expressed, developmentally down-regulated 2)       36774_f_at   up   0.01037535   proline-rich protein BstNI subfamily 1       35764_at   down   0.0104032   oral-facial-digital syndrome 1       35939_s_at   up   0.01040841   POU domain, class 4, transcription factor 1       36807_at   up   0.010412052   TED protein       33034_at   up   0.01042984   rhomboid, veinlet-like 1 ( Drosophila )       36660_at   down   0.010439681   RAB11A, member RAS oncogene family       37031_at   down   0.010449766   chromosome 9 open reading frame 10       39165_at   down   0.010454441   nitrogen fixation cluster-like       32339_at   up   0.010466418   pancreatic polypeptide       540_at   up   0.010490446   heat shock 27 kDa protein 2       31671_at   down   0.010490552   RNA binding motif, single stranded interacting protein 1       40792_s_at   up   0.010508924   triple functional domain (PTPRF interacting)       31423_at   up   0.010540363       34786_at   down   0.010555311   jumonji domain containing 1       32217_at   down   0.010581595   chromosome 12 open reading frame 22       41290_at   up   0.010587378   neural cell adhesion molecule 1       33470_at   up   0.010596187   KIAA1719 protein       39229_at   up   0.010609138   serologically defined colon cancer antigen 1       38209_at   up   0.010647629   prostaglandin E receptor 1 (subtype EP1), 42 kDa       1138_at   up   0.010681017   solute carrier family 20 (phosphate transporter), member 1       41351_at   up   0.010681598   collagen, type VI, alpha 1       38530_at   up   0.010725893   hypothetical protein FLJ22709       32815_at   up   0.010728637       41223_at   down   0.010758437   cytochrome c oxidase subunit Va       39448_r_at   up   0.010786654   B7 gene       38208_at   up   0.010791254   solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc)                   transporter), member A3       33902_at   up   0.010802466   glycerol-3-phosphate dehydrogenase 1 (soluble)       32885_f_at   up   0.010812006   proline-rich protein BstNI subfamily 2       41253_s_at   down   0.010819631   chorionic somatomammotropin hormone 2       32031_at   up   0.010819727   carbamoyl-phosphate synthetase 2, aspartate transcarbamylase,                   and dihydroorotase       38025_r_at   up   0.010821372   rap2 interacting protein x       35510_at   up   0.010831878   sodium channel, voltage gated, type VIII, alpha       32956_at   up   0.010838375   G protein-coupled receptor, family C, group 5, member B       41033_at   down   0.01084462   zinc finger protein 84 (HPF2)       33768_at   up   0.010848796   dystrophia myotonica-containing WD repeat motif       34449_at   up   0.010856436   caspase 2, apoptosis-related cysteine protease (neural precursor                   cell expressed, developmentally down-regulated 2)       31674_s_at   up   0.010905397   bromodomain containing 3       32856_at   up   0.010925156   KIAA0819 protein       1401_g_at   up   0.010933721   colony stimulating factor 2 (granulocyte-macrophage)       35147_at   up   0.010946156   MCF.2 cell line derived transforming sequence-like       924_s_at   down   0.010998105   protein phosphatase 2 (formerly 2A), catalytic subunit, beta                   isoform       40912_s_at   up   0.01100562   biphenyl hydrolase-like (serine hydrolase; breast epithelial mucin-                   associated antigen)       31457_at   up   0.011007906   forkhead box D2       40653_at   up   0.011010145   regulator of G-protein signalling 7       35815_at   down   0.011012092   huntingtin interacting protein B       33690_at   up   0.011014125       32271_at   up   0.011029711   FOS-like antigen 1       35164_at   up   0.011029719   Wolfram syndrome 1 (wolframin)       868_at   down   0.011059405   TAF10 RNA polymerase II, TATA box binding protein (TBP)-                   associated factor, 30 kDa       31949_at   up   0.011111935   Ras protein-specific guanine nucleotide-releasing factor 1       34485_r_at   up   0.011126448   ADP-ribosylation factor guanine nucleotide-exchange factor 2                   (brefeldin A-inhibited)       40189_at   down   0.011156147   SET translocation (myeloid leukemia-associated)       38026_at   up   0.011184842   fibulin 1       32789_at   down   0.01118756   nuclear cap binding protein subunit 2, 20 kDa       2087_s_at   up   0.011265547   cadherin 11, type 2, OB-cadherin (osteoblast)       477_at   up   0.011266133   interferon regulatory factor 5       1619_g_at   up   0.011283533   cytochrome P450, family 19, subfamily A, polypeptide 1       31368_at   up   0.011303022   zinc finger protein 291       35484_at   up   0.011329287       37221_at   down   0.0113471   protein kinase, cAMP-dependent, regulatory, type II, beta       38479_at   down   0.011383491   acidic (leucine-rich) nuclear phosphoprotein 32 family, member B       AFFX-   up   0.011438611       YEL024w/RIP1_at       36061_at   up   0.011458942       1800_g_at   up   0.011481816   excision repair cross-complementing rodent repair deficiency,                   complementation group 4       36052_at   up   0.011487914   adducin 2 (beta)       36201_at   up   0.011488798   glyoxalase I       40032_at   up   0.011543083   KIAA0133 gene product       33539_at   up   0.011546061   myelin expression factor 2       35860_r_at   up   0.011555174       36601_at   down   0.011556615   vinculin       34901_at   up   0.011562757   ubiquitin specific protease 2       31856_at   up   0.011566968   glycoprotein A repetitions predominant       39376_at   down   0.01157243   homeodomain interacting protein kinase 1       37860_at   up   0.011582858   zinc finger protein 337       AFFX-BioDn-5_at   up   0.011589001       34084_at   up   0.011592343   aldo-keto reductase family 1, member D1 (delta 4-3-ketosteroid-5-                   beta-reductase)       32880_at   up   0.01161328   secretoglobin, family 1D, member 2       160038_s_at   up   0.011619181   insulin       37007_at   down   0.011628359   tumor differentially expressed 1       36747_at   up   0.011652598       38882_r_at   up   0.011660597   tripartite motif-containing 16       41724_at   down   0.011675116   accessory protein BAP31       34042_at   up   0.011693218   chondroadherin       37088_at   up   0.011693649   serine/threonine kinase 13 (aurora/IPL1-like)       36452_at   up   0.011707524   synaptopodin       39290_f_at   up   0.011738795   PAI-1 mRNA-binding protein       853_at   down   0.011747537   nuclear factor (erythroid-derived 2)-like 2       36332_at   up   0.011793078   arylalkylamine N-acetyltransferase       32415_at   up   0.011799437   interferon, alpha 5       35659_at   down   0.011837246   interleukin 10 receptor, alpha       38126_at   up   0.011859592   biglycan       37475_at   up   0.011876768   DKFZP434J046 protein       40468_at   down   0.011880956   formin binding protein 1       1218_at   up   0.011899656   nuclear receptor subfamily 2, group F, member 6       34644_at   up   0.011971442   beta-2-microglobulin       40036_at   down   0.011989436   mago-nashi homolog, proliferation-associated ( Drosophila )       33922_at   up   0.012007232   PR domain containing 2, with ZNF domain       34803_at   up   0.012039368   ubiquitin specific protease 12       1235_at   down   0.012045788   tyrosine 3-monooxygenase/tryptophan 5-monooxygenase                   activation protein, zeta polypeptide       40736_at   up   0.012066991   cadherin 17, LI cadherin (liver-intestine)       36967_g_at   up   0.012072207   ankyrin 3, node of Ranvier (ankyrin G)       36829_at   up   0.01208281   period homolog 1 ( Drosophila )       41802_at   up   0.012147295   hypothetical protein FLJ22531       34307_at   down   0.012151793   transmembrane 9 superfamily member 2       1631_at   up   0.012168955       40385_at   up   0.012170497   chemokine (C—C motif) ligand 20       31694_at   up   0.012212301   regulatory solute carrier protein, family 1, member 1       40299_at   up   0.012242936   G-protein coupled receptor       35169_at   up   0.01227325   collagen, type XVI, alpha 1       31474_r_at   down   0.012310633   tankyrase, TRF1-interacting ankyrin-related ADP-ribose                   polymerase       36557_at   up   0.012312191   calcium channel, voltage-dependent, beta 1 subunit       37147_at   up   0.012334348   stem cell growth factor; lymphocyte secreted C-type lectin       36544_at   up   0.012341199       40604_at   down   0.012357898   dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2       37746_r_at   up   0.012358556   suppression of tumorigenicity 5       41101_at   up   0.012390473   Sac domain-containing inositol phosphatase 3       37310_at   up   0.01240215   plasminogen activator, urokinase       32232_at   down   0.012415251   NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5, 16 kDa       AFFX-BioC-5_at   up   0.012424633       32101_at   up   0.01242678   galactosamine (N-acetyl)-6-sulfate sulfatase (Morquio syndrome,                   mucopolysaccharidosis type IVA)       32079_at   up   0.012428316   kinesin family member 13B       38710_at   up   0.01246202   ubiquitin-specific protease otubain 1       40961_at   down   0.012462865   SWI/SNF related, matrix associated, actin dependent regulator of                   chromatin, subfamily a, member 2       32192_g_at   up   0.012473564   ring finger protein 110       38441_s_at   down   0.012487948   membrane cofactor protein (CD46, trophoblast-lymphocyte cross-                   reactive antigen)       36016_at   up   0.012489251   cortistatin       41305_at   up   0.01250619   solute carrier family 5 (sodium/glucose cotransporter), member 2       41289_at   up   0.012530504   neural cell adhesion molecule 1       32613_at   up   0.012539347   synaptic vesicle glycoprotein 2B       31734_at   up   0.012541867   homeo box C11       35163_at   down   0.012560197   KIAA1041 protein       41759_at   down   0.012605139   transcription elongation factor B (SIII), polypeptide 1 pseudogene       37561_at   down   0.012613195   nuclear transcription factor Y, alpha       39627_at   up   0.012650879   early endosome antigen 1, 162 kD       38413_at   down   0.012716582   defender against cell death 1       35473_at   up   0.012718357   collagen, type I, alpha 1       33724_at   up   0.012747577   breast cancer 1, early onset       572_at   up   0.01277828   TTK protein kinase       33937_at   up   0.012832989       35229_at   up   0.012850884   carnitine palmitoyltransferase 1A (liver)       39780_at   down   0.01285708   protein phosphatase 3 (formerly 2B), catalytic subunit, beta                   isoform (calcineurin A beta)       41098_at   up   0.012886931   dishevelled associated activator of morphogenesis 2       38128_at   up   0.012911811   N-acetyltransferase 8 (camello like)       35911_r_at   up   0.012913888   matrix metalloproteinase-like 1       34870_at   up   0.012919562   LIM domain binding 3       31705_at   up   0.012932212   ARS component B       32469_at   down   0.012937069   carcinoembryonic antigen-related cell adhesion molecule 3       33808_at   up   0.012942298   TEA domain family member 3       36652_at   up   0.012968039   uroporphyrinogen III synthase (congenital erythropoietic porphyria       35172_at   down   0.012992358   tyrosylprotein sulfotransferase 2       40186_at   up   0.013034664   dual specificity phosphatase 9       39454_f_at   up   0.013098402   T-cell leukemia, homeobox 2       36922_at   up   0.013121302   ribonucleotide reductase M2 polypeptide       39840_at   up   0.013143318   cysteine knot superfamily 1, BMP antagonist 1       39031_at   up   0.013178811   cytochrome c oxidase subunit VIIa polypeptide 1 (muscle)       1032_at   up   0.013182233   dihydropyrimidine dehydrogenase       37314_at   up   0.013203795   chromosome 14 open reading frame 11       36814_at   down   0.013248989   hypothetical protein KIAA1109       31434_at   up   0.013251593       1523_g_at   up   0.013266534   tyrosine kinase, non-receptor, 1       210_at   up   0.013282218   phospholipase C, beta 2       31450_s_at   up   0.013347747   Ras-like without CAAX 2       35303_at   down   0.013354891   insulin induced gene 1       37042_at   up   0.013358442   hyaluronoglucosaminidase 2       37675_at   down   0.013393808   solute carrier family 25 (mitochondrial carrier; phosphate carrier),                   member 3       40363_r_at   up   0.013426669   nuclear factor of kappa light polypeptide gene enhancer in B-cells                   2 (p49/p100)       745_at   up   0.013436936   transcription elongation factor A (SII), 2       39427_at   down   0.013456646   ubiquinol-cytochrome c reductase binding protein       33267_at   down   0.013514384       32381_at   up   0.013553578   RAR-related orphan receptor B       31626_i_at   up   0.013564285   amine oxidase pseudogene       39469_s_at   up   0.013613609   ATPase, aminophospholipid transporter-like, Class I, type 8A,                   member 2       1950_s_at   up   0.013677073   MAD, mothers against decapentaplegic homolog 3 ( Drosophila )       40512_at   up   0.01367746   chimerin (chimaerin) 1       37729_at   down   0.013682129   exportin 1 (CRM1 homolog, yeast)       40402_at   up   0.013695808   solute carrier family 6 (neurotransmitter transporter, noradrenalin)                   member 2       40595_at   up   0.01373059   Treacher Collins-Franceschetti syndrome 1       37756_at   up   0.01375692   RYK receptor-like tyrosine kinase       1664_at   up   0.01381471       31636_s_at   up   0.013826343   solute carrier family 18 (vesicular acetylcholine), member 3       41293_at   up   0.013828112   keratin 7       33546_at   up   0.013836831       31386_at   up   0.013843476   immunoglobulin kappa variable 1/OR15-118       33495_at   up   0.013909579   protein tyrosine phosphatase, receptor type, f polypeptide                   (PTPRF), interacting protein (liprin), alpha 2       37274_at   up   0.013914109   biotinidase       41488_at   down   0.013928912   hypothetical protein A-211C6.1       31999_at   up   0.013935691   ATP-binding cassette, sub-family A (ABC1), member 1       39360_at   down   0.013945505   sorting nexin 3       34791_at   down   0.013953726   t-complex 1       34324_at   down   0.01395827   ceroid-lipofuscinosis, neuronal 5       40819_at   up   0.013958858   RNA binding motif protein 8A       41529_g_at   down   0.013984956       35793_at   down   0.014000217   Ras-GTPase activating protein SH3 domain-binding protein 2       36075_at   up   0.014076733   RAB, member of RAS oncogene family-like 4       33322_i_at   up   0.014082655   stratifin       35978_at   up   0.014105216   proline-rich Gla (G-carboxyglutamic acid) polypeptide 1       37961_at   up   0.014113688   phosphoinositide-3-kinase, regulatory subunit, polypeptide 3 (p55,                   gamma)       35521_at   up   0.01411609   claudin 9       33266_at   up   0.014136389   serine/threonine kinase 12       31325_at   up   0.014137098       41001_at   up   0.014148684   likely ortholog of mouse rabphilin 3A       41123_s_at   up   0.014166567   ectonucleotide pyrophosphatase/phosphodiesterase 2 (autotaxin)       41079_at   up   0.014179586   amiloride-sensitive cation channel 3, testis       33221_at   up   0.014203535   PAX transcription activation domain interacting protein 1 like       806_at   up   0.014209175   cytokine-inducible kinase       39657_at   up   0.014284559   keratin 4       36625_at   up   0.014320189   peroxisomal long-chain acyl-coA thioesterase       38538_at   up   0.014353625   solute carrier family 24 (sodium/potassium/calcium exchanger),                   member 1       37189_at   up   0.014377897   phosphomannomutase 1       33670_at   up   0.014395478       41602_at   up   0.014427132   hippocalcin       39490_f_at   up   0.014434597   ADP-ribosylation factor GTPase activating protein 3       39137_at   up   0.014438261   nuclear factor related to kappa B binding protein       32104_i_at   up   0.014440307   calcium/calmodulin-dependent protein kinase (CaM kinase) II                   gamma       37976_at   up   0.014454216   Ig superfamily protein       36420_at   up   0.014470534   intersectin 2       37204_at   up   0.014470631   pre-alpha (globulin) inhibitor, H3 polypeptide       742_at   up   0.014501825   hyaluronan binding protein 2       277_at   down   0.014527659   myeloid cell leukemia sequence 1 (BCL2-related)       40945_at   up   0.014552217   TGFB inducible early growth response 2       31833_at   up   0.014573625   phosphatidylinositol-4-phosphate 5-kinase, type I, alpha       36913_at   down   0.014582499   stem-loop (histone) binding protein       33783_at   up   0.014601433   plexin B1       34764_at   up   0.014611105   leucyl-tRNA synthetase, mitochondrial       32269_at   up   0.014621549   BAI1-associated protein 1       912_s_at   up   0.014641028   phospholipase A2, group IB (pancreas)       37227_at   up   0.014654821   apoptotic protease activating factor       33440_at   down   0.014672964   transcription factor 8 (represses interleukin 2 expression)       38943_at   down   0.014708654   holocytochrome c synthase (cytochrome c heme-lyase)       35113_at   up   0.014808127   solute carrier family 22 (organic cation transporter), member 1       38181_at   up   0.014820162   matrix metalloproteinase 11 (stromelysin 3)       41018_at   up   0.014823451   DKFZP564O243 protein       35266_at   down   0.014833914   bladder cancer associated protein       463_g_at   up   0.014919402   nuclear factor I/B       33545_at   up   0.014947629   sodium channel, voltage-gated, type IV, alpha       41785_at   down   0.014955497   eukaryotic translation initiation factor 4 gamma, 2       37905_r_at   up   0.015015551       39564_s_at   up   0.015051374   ATP-binding cassette, sub-family B (MDR/TAP), member 6       35342_at   down   0.015052012       36378_at   up   0.015073855   uroplakin 1A       35434_at   up   0.015123449   MADS box transcription enhancer factor 2, polypeptide D                   (myocyte enhancer factor 2D)       41525_at   up   0.015136461   high-mobility group 20B       37276_at   down   0.015149254   IQ motif containing GTPase activating protein 2       1424_s_at   down   0.015163256   tyrosine 3-monooxygenase/tryptophan 5-monooxygenase                   activation protein, eta polypeptide       37442_at   down   0.015178917   hypothetical protein DKFZp586I1420       39214_at   up   0.015195618   plexin B3       36720_at   up   0.015223928   pyruvate dehydrogenase kinase, isoenzyme 3       40941_at   up   0.015261702   VAMP (vesicle-associated membrane protein)-associated protein                   B and C       33374_at   up   0.015278411   complement component 2       40027_at   down   0.015289109   ATP synthase, H+ transporting, mitochondrial F0 complex, subun                   s (factor B)       31738_at   up   0.015316801       33642_s_at   up   0.015319584   solute carrier family 6 (neurotransmitter transporter, creatine),                   member 8       34525_at   up   0.015328652   T-cell leukemia/lymphoma 1B       34923_at   up   0.015331205   KIAA0522 protein       36718_s_at   down   0.015337288   pyruvate dehydrogenase kinase, isoenzyme 3       33666_at   down   0.015344184   heterogeneous nuclear ribonucleoprotein C (C1/C2)       39383_at   up   0.015367512   adenylate cyclase 6       37248_at   up   0.015368335   carboxypeptidase Z       33807_at   up   0.015395268   phosphoinositol 3-phosphate-binding protein-3       1971_g_at   up   0.015433856   fragile histidine triad gene       32522_f_at   up   0.015452907   clathrin, light polypeptide (Lcb)       40237_at   up   0.015487652   tumor suppressing subtransferable candidate 3       35295_g_at   down   0.01549105   Sjogren syndrome antigen A2 (60 kDa, ribonucleoprotein                   autoantigen SS-A/Ro)       218_at   down   0.015538652   IK cytokine, down-regulator of HLA II       39639_s_at   up   0.015540109   transition protein 1 (during histone to protamine replacement)       33144_at   up   0.015542466   solute carrier family 16 (monocarboxylic acid transporters),                   member 3       34697_at   up   0.015588844   low density lipoprotein receptor-related protein 6       39868_at   up   0.015598787   poly(rC) binding protein 3       35091_at   up   0.015609298   neuregulin 2       1096_g_at   up   0.015618275   CD19 antigen       31452_at   up   0.015629582   survival motor neuron pseudogene       39511_at   up   0.015634398   myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog,                     Drosophila ); translocated to, 4       36826_at   up   0.015634839   general transcription factor IIF, polypeptide 1, 74 kDa       1415_at   up   0.015636698   embryonal Fyn-associated substrate       41279_f_at   up   0.015657636   mitogen-activated protein kinase 8 interacting protein 1       36326_at   up   0.015683908   nescient helix loop helix 2       1555_f_at   up   0.015707626   cytochrome P450, family 2, subfamily A, polypeptide 7       37133_at   up   0.015716843   serine/threonine kinase 23       33610_at   up   0.015729266   claudin 8       40674_s_at   up   0.015769271   homeo box C6       39765_at   up   0.015769941   talin 2       35352_at   up   0.015775962   aryl-hydrocarbon receptor nuclear translocator 2       35974_at   down   0.015787229   lymphoid-restricted membrane protein       34802_at   up   0.015795589   collagen, type VI, alpha 2       34902_at   up   0.015815292   KIAA0492 protein       984_g_at   up   0.015817247   mitogen-activated protein kinase 12       37267_at   up   0.015828594   thimet oligopeptidase 1       34002_at   up   0.0158432   hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-                   isomerase 2       38946_at   up   0.015843586   protein phosphatase, EF hand calcium-binding domain 1       31704_at   up   0.015883818   deoxyribonuclease I-like 2       41042_r_at   up   0.01592032   myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))       31926_at   up   0.01593408   cytochrome P450, family 7, subfamily A, polypeptide 1       37158_at   up   0.015948773       1896_s_at   up   0.015958981   ATP-binding cassette, sub-family C (CFTR/MRP), member 1       41416_at   up   0.015961067   fibrinogen-like 1       35910_f_at   up   0.015964906   matrix metalloproteinase-like 1       38582_at   up   0.015969003   serine protease inhibitor, Kazal type 1       38114_at   down   0.016076891   RAD21 homolog ( S. pombe )       40926_at   up   0.016084766   solute carrier family 6 (neurotransmitter transporter, creatine),                   member 8       34394_at   down   0.01609586   activity-dependent neuroprotector       31556_at   up   0.016136864       32103_at   up   0.016177838   serine (or cysteine) proteinase inhibitor, clade F (alpha-2                   antiplasmin, pigment epithelium derived factor), member 2       38572_at   up   0.016177861   FGFR1 oncogene partner       34864_at   up   0.016199781   hypothetical protein CGI-57       35095_r_at   down   0.016220568   leukocyte immunoglobulin-like receptor, subfamily A (without TM                   domain), member 3       1391_s_at   up   0.016223701   cytochrome P450, family 4, subfamily A, polypeptide 11       31902_at   up   0.016232561   deiodinase, iodothyronine, type II       37303_at   down   0.016339359   ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-                   like 1       38841_at   down   0.016345714   putative glialblastoma cell differentiation-related       32204_at   up   0.016360734   phosphodiesterase 6G, cGMP-specific, rod, gamma       37060_at   up   0.016378817       31577_at   up   0.016382282   collagen, type XIX, alpha 1       40180_at   up   0.016385547   insulin receptor substrate 2       39775_at   up   0.016407009   serine (or cysteine) proteinase inhibitor, clade G (C1 inhibitor),                   member 1, (angioedema, hereditary)       41143_at   down   0.016409508   calmodulin 1 (phosphorylase kinase, delta)       36583_at   down   0.016418131   sorting nexin 1       35828_at   up   0.016423982   cysteine-rich protein 2       37573_at   up   0.016431244   angiopoietin-like 2       39784_at   down   0.016449639   eukaryotic translation initiation factor 2, subunit 1 alpha, 35 kDa       40745_at   up   0.016531089   adaptor-related protein complex 1, beta 1 subunit       36987_at   up   0.016535539   lamin B2       35565_at   up   0.016616751   LanC lantibiotic synthetase component C-like 2 (bacterial)       37672_at   down   0.016674897   ubiquitin specific protease 7 (herpes virus-associated)       39103_s_at   up   0.016676884       37554_at   up   0.016679024   kallikrein 6 (neurosin, zyme)       38657_s_at   up   0.016700888   clathrin, light polypeptide (Lca)       36019_at   up   0.016718156   serine/threonine kinase 19       34214_at   up   0.016732911   KIAA0644 gene product       36844_at   up   0.016756145   dedicator of cyto-kinesis 3       41711_at   up   0.016773547   thioredoxin reductase 2       939_at   up   0.016782506       35396_at   up   0.016794613   hyaluronan synthase 2       35198_at   up   0.016796595   promethin       33947_at   up   0.016809014   G protein-coupled receptor 3       38840_s_at   down   0.01682395   profilin 2       31890_s_at   down   0.016843461   zinc finger protein 143 (clone pHZ-1)       34024_at   up   0.016873841   chloride channel 5 (nephrolithiasis 2, X-linked, Dent disease)       37146_at   down   0.016887348   KIAA0404 protein       39801_at   up   0.01689521   procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3       40879_at   down   0.016929255   coiled-coil protein BICD2       33595_r_at   up   0.016932374   recombination activating gene 2       706_at   down   0.016934279       35798_at   up   0.01694392   NS1-associated protein 1       1713_s_at   down   0.016952268   cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits                   CDK4)       35112_at   up   0.016979898   regulator of G-protein signalling 9       32163_f_at   up   0.016998487   chorionic somatomammotropin hormone 2       31881_at   down   0.017004901   mob protein       31775_at   up   0.017053345   surfactant, pulmonary-associated protein D       37995_s_at   down   0.017056726   fragile X mental retardation 1       35915_at   up   0.017078706   inhibin, beta C       36896_s_at   down   0.017114074   aryl hydrocarbon receptor nuclear translocator-like       34222_at   up   0.017137337   hypothetical protein from clone 24828       39194_at   up   0.017213039   glutathione peroxidase 2 (gastrointestinal)       33879_at   up   0.017232449   type I sigma receptor       36152_at   up   0.017242899   GDP dissociation inhibitor 1       263_g_at   down   0.017262681   adenosylmethionine decarboxylase 1       36690_at   down   0.017262777   nuclear receptor subfamily 3, group C, member 1 (glucocorticoid                   receptor)       35398_at   up   0.017273339       38046_at   down   0.017297027   IK cytokine, down-regulator of HLA II       1483_at   up   0.017308878   cadherin 4, type 1, R-cadherin (retinal)       34567_at   up   0.017357311   cylicin, basic protein of sperm head cytoskeleton 2       33122_at   up   0.017373574   regulator of G-protein signalling 10       884_at   up   0.017392757   integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3                   receptor)       35080_at   up   0.017429659   neurotensin receptor 1 (high affinity)       2022_at   up   0.017431884   v-akt murine thymoma viral oncogene homolog 2       40535_i_at   up   0.017441987   translation initiation factor IF2       32587_at   down   0.017445795   zinc finger protein 36, C3H type-like 2       1399_at   down   0.017450684   transcription elongation factor B (SIII), polypeptide 1 (15 kDa,                   elongin C)       1169_at   up   0.017478787   protocadherin gamma subfamily B, 7       41285_at   up   0.017525434   inositol polyphosphate-5-phosphatase, 40 kDa       37228_at   up   0.017538384   polo-like kinase ( Drosophila )       35876_s_at   up   0.017574915   sphingosine-1-phosphate lyase 1       32903_at   up   0.017581104   transforming growth factor, beta receptor I (activin A receptor type                   II-like kinase, 53 kDa)       35180_at   down   0.017588189   c-Mpl binding protein       1051_g_at   up   0.017597054   melan-A       33126_at   down   0.017609759   glycosyltransferase AD-017       33436_at   up   0.017614337   SRY (sex determining region Y)-box 9 (campomelic dysplasia,                   autosomal sex-reversal)       33806_at   up   0.01762397   hypothetical protein FLJ22195       39965_at   up   0.01764993   ras-related C3 botulinum toxin substrate 3 (rho family, small GTF                   binding protein Rac3)       385_at   up   0.017687295       40959_at   up   0.017704581   KIAA0599 protein       36356_at   up   0.017780577   growth differentiation factor 5 (cartilage-derived morphogenetic                   protein-1)       39855_at   up   0.017795155   Fzr1 protein       40931_at   down   0.017817731   CGI-100 protein       492_g_at   up   0.017826554   protein tyrosine phosphatase, receptor type, G       1420_s_at   down   0.017834415   eukaryotic translation initiation factor 4A, isoform 2       36407_at   up   0.017841019   kallikrein 13       37185_at   up   0.017841095   serine (or cysteine) proteinase inhibitor, clade B (ovalbumin),                   member 2       40872_at   down   0.017872198   cytochrome c oxidase subunit VIb       37334_at   down   0.017882062   heterogeneous nuclear ribonucleoprotein A0       39185_at   down   0.017885168   hypothetical protein 628       37766_s_at   down   0.017887937   proteasome (prosome, macropain) 26S subunit, ATPase, 5       32005_at   up   0.017891687   pro-melanin-concentrating hormone       31688_at   up   0.017957105   skin-specific protein       2055_s_at   up   0.01796478   integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen                   CD29 includes MDF2, MSK12)       35214_at   up   0.018093625   UDP-glucose dehydrogenase       34161_at   up   0.018130162   lactoperoxidase       36392_at   up   0.018158369   zinc finger protein 135 (clone pHZ-17)       33310_at   down   0.018160642   comparative gene identification 58       38298_at   up   0.018174474   potassium large conductance calcium-activated channel,                   subfamily M, beta member 1       39200_s_at   up   0.018250192   growth differentiation factor 11       625_at   up   0.018283211   vesicle amine transport protein 1 homolog ( T californica )       36834_at   up   0.018291464   DKFZP564G202 protein       40950_at   up   0.018330724   dynein, cytoplasmic, light intermediate polypeptide 2       35790_at   down   0.018330827   vacuolar protein sorting 26 (yeast)       38915_at   up   0.018336984   KIAA0563 gene product       41394_at   up   0.018360549   phospholipase D2       33961_at   up   0.018361619       37602_at   up   0.018387236   guanidinoacetate N-methyltransferase       507_s_at   down   0.018388413   E74-like factor 2 (ets domain transcription factor)       31637_s_at   up   0.018396658   nuclear receptor subfamily 1, group D, member 1       36797_at   up   0.018409859   sialophorin (gpL115, leukosialin, CD43)       39345_at   down   0.018412516   Niemann-Pick disease, type C2       40188_f_at   up   0.018416817       38374_at   down   0.018474391   TGFB inducible early growth response       38104_at   down   0.018535035   2,4-dienoyl CoA reductase 1, mitochondrial       35354_at   up   0.018538623   synaptogyrin 1       34336_at   down   0.018562306   lysyl-tRNA synthetase       38526_at   up   0.01860093   phosphodiesterase 4D, cAMP-specific (phosphodiesterase E3                   dunce homolog,  Drosophila )       36032_at   down   0.018630726   HSPCO34 protein       35485_at   up   0.01866013   glutamate receptor, metabotropic 4       39547_at   up   0.018672308   RAN binding protein 9       37875_at   up   0.018679056   glycoprotein A33 (transmembrane)       730_r_at   up   0.018699817       33985_s_at   up   0.018705931   heat shock 90 kDa protein 1, beta       39319_at   down   0.018716388   lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte                   protein of 76 kDa)       40094_r_at   up   0.018725325   Lutheran blood group (Auberger b antigen included)       36924_r_at   up   0.018756701   secretogranin II (chromogranin C)       36306_at   up   0.018756705   potassium voltage-gated channel, KQT-like subfamily, member 3       1704_at   up   0.018767596   vav 2 oncogene       41399_at   down   0.018773794   KIAA1111 protein       40804_at   up   0.01880313   nucleoporin 88 kDa       31837_at   up   0.018865712   hypothetical protein BC002942       35725_at   down   0.018871291   karyopherin alpha 3 (importin alpha 4)       38154_at   up   0.018880449       39140_at   down   0.018895051   nucleic acid helicase DDXx       34055_at   up   0.018918709   activin A receptor, type IB       41804_at   up   0.018951167   hypothetical protein FLJ22531       31701_r_at   up   0.018965341   B1 for mucin       32909_at   up   0.019004154   aquaporin 5       32399_at   up   0.019021041   ecotropic viral integration site 1       40496_at   up   0.01903891   complement component 1, s subcomponent       36330_at   up   0.019050873   cysteine conjugate-beta lyase; cytoplasmic (glutamine                   transaminase K, kyneurenine aminotransferase)       888_s_at   up   0.019070811   LAG1 longevity assurance homolog 1 ( S. cerevisiae )       37748_at   down   0.019075149   KIAA0232 gene product       41418_at   up   0.019075413   latrophilin 1       40488_at   up   0.019080462   dystrophin (muscular dystrophy, Duchenne and Becker types)       40390_at   up   0.01908294   serine dehydratase       41078_at   up   0.019088607   KIAA0150 protein       38626_at   down   0.019091364   KIAA0399 protein       650_s_at   down   0.019102817   calcium/calmodulin-dependent protein kinase (CaM kinase) II                   gamma       39245_at   up   0.019111468       36080_at   up   0.0191278   clock homolog (mouse)       39408_at   up   0.019130961   hypothetical protein MGC5139       39872_at   up   0.019146391   G-2 and S-phase expressed 1       36119_at   up   0.019160158   caveolin 1, caveolae protein, 22 kDa       36570_at   up   0.019170443   calbindin 1, 28 kDa       40063_at   down   0.01917505   nuclear domain 10 protein       39113_at   up   0.019182305   protein disulfide isomerase related protein (calcium-binding                   protein, intestinal-related)       36663_at   up   0.019184809   natriuretic peptide precursor A       34573_at   up   0.019216743   ephrin-A3       37615_at   up   0.019228832   growth factor receptor-bound protein 10       34306_at   down   0.019238039   muscleblind-like ( Drosophila )       40344_at   up   0.019239373   neuroligin 1       36375_at   up   0.019280928   outer dense fiber of sperm tails 1       32975_g_at   up   0.01928292   homolog of Yeast RRP4 (ribosomal RNA processing 4), 3′-5′-                   exoribonuclease       692_s_at   up   0.01928419   superoxide dismutase 3, extracellular       38088_r_at   up   0.019334463   S100 calcium binding protein A4 (calcium protein, calvasculin,                   metastasin, murine placental homolog)       36139_at   up   0.01937145   chromosome 6 open reading frame 4       33329_at   up   0.019378158   nuclear factor I/C (CCAAT-binding transcription factor)       35598_at   up   0.019416892   histone 1, H3e       35821_at   down   0.019431843   histone deacetylase 3       41241_at   down   0.019435076   asparaginyl-tRNA synthetase       667_at   up   0.019461528   arginine vasopressin receptor 2 (nephrogenic diabetes insipidus)       39809_at   down   0.019462445   HMG-box containing protein 1       34851_at   up   0.019463854   serine/threonine kinase 6       1007_s_at   up   0.0194894   discoidin domain receptor family, member 1       567_s_at   up   0.01953774   promyelocytic leukemia       40355_at   up   0.019595751   AND-1 protein       37562_at   up   0.019609089   protocadherin 1 (cadherin-like 1)       39451_i_at   up   0.019623483   iduronate 2-sulfatase (Hunter syndrome)       32785_at   down   0.019631759   eukaryotic translation initiation factor 3, subunit 10 theta,                   150/170 kDa       694_at   up   0.019702348       36276_at   up   0.019710749   contactin 2 (axonal)       668_s_at   up   0.019731276   matrix metalloproteinase 7 (matrilysin, uterine)       31468_f_at   up   0.019744635   glutamate receptor, metabotropic 1       40418_at   down   0.019762763   retinoblastoma binding protein 4       36051_s_at   up   0.01982094   adducin 2 (beta)       34667_at   up   0.019830749   nuclear transcription factor, X-box binding 1       37565_at   down   0.019838268   monocyte to macrophage differentiation-associated       36954_at   down   0.019858282   KIAA0218 gene product       31746_at   up   0.019892901   zinc finger protein 204       1481_at   up   0.019894049   matrix metalloproteinase 12 (macrophage elastase)       666_at   up   0.019910172   phosphodiesterase 4A, cAMP-specific (phosphodiesterase E2                   dunce homolog,  Drosophila )       1141_at   up   0.019912154   melanocortin 5 receptor       39037_at   down   0.019935896   myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog,                     Drosophila ); translocated to, 2       33673_r_at   up   0.019947098   UDP glycosyltransferase 2 family, polypeptide B17       33652_at   up   0.019972991   a disintegrin and metalloproteinase domain 20       35534_at   up   0.020002103   KIAA0514 gene product       34824_at   down   0.020009104   ubiquilin 2       39108_at   up   0.020020999   lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)       31810_g_at   up   0.020025692   contactin 1       32595_at   down   0.02002983   G-rich RNA sequence binding factor 1       33345_at   up   0.020031007   kinesin family member 3C       39294_at   up   0.020106081   nuclear receptor subfamily 2, group F, member 1       1834_at   up   0.02010754   putative G protein coupled receptor       33622_at   up   0.020119043   calcium channel, voltage-dependent, L type, alpha 1C subunit       40598_at   up   0.020139375   START domain containing 5       34846_at   up   0.020142879   calcium/calmodulin-dependent protein kinase (CaM kinase) II beta       32928_at   up   0.020150947   POU domain, class 2, transcription factor 3       37073_at   up   0.020168835   eyes absent homolog 1 ( Drosophila )       41784_at   down   0.020217509   SR rich protein       34184_at   up   0.020259848   adenomatous polyposis coli like       38477_at   down   0.020271492   diptheria toxin resistance protein required for diphthamide                   biosynthesis-like 1 ( S. cerevisiae )       40260_g_at   up   0.020317242   RNA binding motif protein 9       40740_at   up   0.020333636   paired box gene 6 (aniridia, keratitis)       36007_at   up   0.020396168   DKFZP586L151 protein       36380_at   up   0.020398685   DKFZP434F122 protein       41574_at   down   0.020400712   pinin, desmosome associated protein       39879_s_at   up   0.020473075   hypothetical protein FLJ10120       33787_at   up   0.020483026   KIAA0537 gene product       33008_at   up   0.020521776   olfactory receptor, family 7, subfamily E, member 24 pseudogene       33294_at   down   0.020522678   KIAA0116 protein       33241_at   down   0.020533956   KIAA0626 gene product       35584_s_at   up   0.020544608   calcium channel, voltage-dependent, alpha 1F subunit       36355_at   up   0.02055766   involucrin       33681_at   up   0.020563179   serine (or cysteine) proteinase inhibitor, clade H (heat shock                   protein 47), member 1, (collagen binding protein 1)       33558_at   up   0.020601885   T-box 5       34778_at   up   0.020605113       33319_at   down   0.02062051   axin 1       33150_at   down   0.020623787   disrupter of silencing 10       1549_s_at   up   0.02062695   serine (or cysteine) proteinase inhibitor, clade B (ovalbumin),                   member 4       34274_at   down   0.020627926   RNA binding motif protein 16       32637_r_at   up   0.020660502   PI-3-kinase-related kinase SMG-1       37201_at   up   0.020782803   inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive                   glycoprotein)       40003_at   up   0.020809717   glycoprotein 2 (zymogen granule membrane)       38605_at   down   0.020824508   NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 1, 7 kDa       36775_f_at   up   0.020845451   proline-rich protein BstNI subfamily 2       1557_at   down   0.020870386   p21/Cdc42/Rac1-activated kinase 1 (STE20 homolog, yeast)       1371_s_at   up   0.02094109   cytochrome P450, family 2, subfamily B, polypeptide 6       504_at   down   0.020955749   ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast)       36074_at   up   0.02103264   imprinted in Prader-Willi syndrome       41335_at   down   0.021053426   DKFZP566O1646 protein       37337_at   down   0.021053683   small nuclear ribonucleoprotein polypeptide G       34381_at   down   0.02108904   cytochrome c oxidase subunit VIIc       36640_at   up   0.021092759   myosin, light polypeptide 2, regulatory, cardiac, slow       36580_at   down   0.02112571   hypothetical protein FLJ13910       34172_s_at   up   0.021127469   DNA segment on chromosome X and Y (unique) 155 expressed                   sequence       37490_at   up   0.021147824   solute carrier family 4, anion exchanger, member 3       40454_at   up   0.021159268   FAT tumor suppressor homolog 1 ( Drosophila )       37541_at   up   0.021166157   selectin P ligand       40261_at   up   0.021175781   RNA binding motif protein 9       32463_at   up   0.021175784   Rho GTPase activating protein 6       38146_at   up   0.021176618   suppression of tumorigenicity 18 (breast carcinoma) (zinc finger                   protein)       34495_r_at   up   0.021186298   synaptogyrin 4       32850_at   down   0.021186976   nucleoporin 153 kDa       38963_i_at   up   0.021187774   Wiskott-Aldrich syndrome (eczema-thrombocytopenia)       365_at   up   0.021193084   cylicin, basic protein of sperm head cytoskeleton 1       35276_at   up   0.02120371   claudin 4       33875_at   down   0.021227384   ATPase, H+ transporting, lysosomal 9 kDa, V0 subunit e       36729_g_at   up   0.02125517   adrenergic, alpha-1D-, receptor       34922_at   up   0.02126488   cadherin 19, type 2       41425_at   down   0.021323848   Friend leukemia virus integration 1       41256_at   down   0.021325224   eukaryotic translation elongation factor 1 delta (guanine nucleotid                   exchange protein)       39341_at   up   0.021340838   thyroid hormone receptor interactor 6       40558_at   up   0.021360635   guanylate cyclase activator 1B (retina)       41086_at   up   0.021365747   regulator of G-protein signalling 20       38592_s_at   up   0.021377698   KIAA0284 protein       41347_at   up   0.021382759   iroquois homeobox protein 5       40411_at   down   0.021393313   nuclear receptor coactivator 6       1344_at   up   0.02140639   paired box gene 3 (Waardenburg syndrome 1)       38117_at   up   0.021409201   SEC24 related gene family, member C ( S. cerevisiae )       34147_g_at   up   0.021417061   8-oxoguanine DNA glycosylase       33363_at   up   0.021424419   JTV1 gene       39966_at   up   0.021450725   chondroitin sulfate proteoglycan 5 (neuroglycan C)       38499_s_at   up   0.021471019   myelin-associated oligodendrocyte basic protein       39914_r_at   up   0.02147462   transient receptor potential cation channel, subfamily M, member 2       36271_at   up   0.021478981   KIAA1024 protein       40017_at   up   0.021500608   DKFZP586H2123 protein       40141_at   down   0.021547278   cullin 4B       39857_at   down   0.021570023   syntaxin 11       34708_at   up   0.021612712   ficolin (collagen/fibrinogen domain containing) 3 (Hakata antigen)       40111_g_at   up   0.02161511   isocitrate dehydrogenase 3 (NAD+) beta       38779_r_at   up   0.021635798   hepatoma-derived growth factor (high-mobility group protein 1-                   like)       41705_at   up   0.021662157   radical fringe homolog ( Drosophila )       35533_f_at   up   0.021728712   killer cell lectin-like receptor subfamily C, member 4       34682_at   up   0.021746147   hypothetical protein DKFZp566H0824       40484_g_at   up   0.021753668   transcriptional activator of the c-fos promoter       37600_at   up   0.021776035   extracellular matrix protein 1       41830_at   down   0.021821477   KIAA0494 gene product       32293_at   up   0.021838004   luteinizing hormone/choriogonadotropin receptor       38512_r_at   up   0.02189719   ELAV (embryonic lethal, abnormal vision,  Drosophila )-like 3 (Hu                   antigen C)       31585_at   up   0.021930368   glutamate receptor, metabotropic 7       38096_f_at   down   0.021970254   major histocompatibility complex, class II, DP beta 1       39792_at   down   0.021996389   heterogeneous nuclear ribonucleoprotein R       33863_at   up   0.022049912   hypoxia up-regulated 1       40596_at   up   0.022092324   Treacher Collins-Franceschetti syndrome 1       32969_r_at   up   0.022103816   VGF nerve growth factor inducible       39803_s_at   up   0.022127147   chromosome 21 open reading frame 2       38229_at   up   0.02213322   cytochrome P450, family 3, subfamily A, polypeptide 5                   pseudogene 2       32316_s_at   down   0.022134897   heat shock 90 kDa protein 1, alpha       32414_at   up   0.022161556       35037_at   up   0.022179733   solute carrier family 28 (sodium-coupled nucleoside transporter),                   member 1       34502_g_at   up   0.022183005   runt-related transcription factor 2       1744_at   up   0.022223723       36722_s_at   up   0.022234623   hepatocyte nuclear factor 4, alpha       35403_at   down   0.022253864   KIAA1094 protein       41553_at   up   0.022276095   chromosome 8 open reading frame 1       31904_at   up   0.022323192   phosphodiesterase 2A, cGMP-stimulated       1453_at   down   0.022339505   MAD, mothers against decapentaplegic homolog 2 ( Drosophila )       271_s_at   up   0.022347943   cathepsin E       35193_at   down   0.022417379   chromosome condensation 1-like       1766_g_at   up   0.022422468   caspase 10, apoptosis-related cysteine protease       1890_at   up   0.022429583   prostate differentiation factor       346_s_at   up   0.022432014   angiotensin II receptor, type 1       36209_at   down   0.022446797   bromodomain containing 2       1271_g_at   up   0.022453783   v-rel reticuloendotheliosis viral oncogene homolog A, nuclear                   factor of kappa light polypeptide gene enhancer in B-cells 3, p65                   (avian)       1608_at   up   0.022472991       36168_at   up   0.022480506   fibroblast growth factor receptor 1 (fms-related tyrosine kinase 2,                   Pfeiffer syndrome)       32014_at   up   0.022498779   a disintegrin and metalloproteinase domain 18       161_at   up   0.022524961   RAB9, member RAS oncogene family, pseudogene 1       313_at   up   0.022571235       37466_at   down   0.022589707   RAB7, member RAS oncogene family-like 1       31521_f_at   down   0.02267027   histone 1, H4j       40378_at   up   0.02267704   SH3-domain GRB2-like 2       160037_at   up   0.022764551   matrix metalloproteinase 15 (membrane-inserted)       31879_at   down   0.022766829   far upstream element (FUSE) binding protein 3       780_at   up   0.022771077   runt-related transcription factor 1 (acute myeloid leukemia 1; aml1                   oncogene)       39234_at   up   0.02279868   DKFZP586I111 protein       1675_at   down   0.022841517   RAS p21 protein activator (GTPase activating protein) 1       37328_at   down   0.022861457   pleckstrin       32952_at   up   0.0228892   Retina-derived POU-domain factor-1       34582_at   up   0.022906704   solute carrier family 1 (glial high affinity glutamate transporter),                   member 2       38224_at   up   0.022931589   small nuclear RNA activating complex, polypeptide 3, 50 kDa       32811_at   up   0.022951758   myosin IC       33463_at   up   0.022978048   xanthine dehydrogenase       40830_at   up   0.023005272   DnaJ (Hsp40) homolog, subfamily C, member 4       39913_at   up   0.023012464   heparan sulfate 6-O-sulfotransferase 1       1577_at   up   0.023034692   androgen receptor (dihydrotestosterone receptor; testicular                   feminization; spinal and bulbar muscular atrophy; Kennedy                   disease)       38452_at   up   0.023045399   hypothetical protein MGC5466       37482_at   up   0.023062615   aldo-keto reductase family 1, member B10 (aldose reductase)       33471_g_at   up   0.023074443   KIAA1719 protein       40322_at   up   0.023076512   interleukin 1 receptor-like 1       41871_at   up   0.023125317   lung type-I cell membrane-associated glycoprotein       1598_g_at   up   0.023128654   growth arrest-specific 6       38160_at   down   0.023139429   lymphocyte antigen 75       120_at   up   0.02321075   integrin, alpha 1       32947_at   up   0.023220361   sodium channel, voltage-gated, type IX, alpha       38199_at   up   0.023220366   similar to RIKEN cDNA 2610307I21       32047_at   up   0.023234807   DNA fragmentation factor, 45 kDa, alpha polypeptide       32080_at   up   0.023277114   tetracycline transporter-like protein       39483_s_at   down   0.023286561   integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen                   CD29 includes MDF2, MSK12)       40083_at   down   0.023290559   KIAA0625 protein       39832_at   up   0.02332293   arsenate resistance protein ARS2       1627_at   up   0.02332432       2032_s_at   up   0.023358429   integrin, alpha V (vitronectin receptor, alpha polypeptide, antigen                   CD51)       32100_r_at   up   0.023383121   galactosamine (N-acetyl)-6-sulfate sulfatase (Morquio syndrome,                   mucopolysaccharidosis type IVA)       35644_at   up   0.023398424   hephaestin       38901_at   up   0.023439148   ubiquitin specific protease 19       40183_at   up   0.023444505   coactivator-associated arginine methyltransferase-1       222_at   up   0.023456142   exostoses (multiple) 1       36327_at   up   0.023463563   potassium inwardly-rectifying channel, subfamily J, member 1       32329_at   up   0.023467672   keratin, hair, basic, 6 (monilethrix)       34166_at   up   0.023483105   solute carrier family 6 (neurotransmitter transporter, L-proline),                   member 7       37690_at   up   0.023498915   ilvB (bacterial acetolactate synthase)-like       40856_at   up   0.023527316   serine (or cysteine) proteinase inhibitor, clade F (alpha-2                   antiplasmin, pigment epithelium derived factor), member 1       31740_s_at   up   0.023574982   paired box gene 4       40315_at   up   0.023606902   serine protease inhibitor, Kazal type, 5       40085_s_at   down   0.023614131   transcription factor CP2       32620_at   up   0.023615667   fetuin B       36972_at   down   0.023647274   coated vesicle membrane protein       37784_at   up   0.023651963       37172_at   up   0.023681682   carboxypeptidase B2 (plasma, carboxypeptidase U)       39412_at   up   0.023685437   tripartite motif-containing 26       33197_at   up   0.023691092   myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))       39876_at   up   0.023730024   ectonucleoside triphosphate diphosphohydrolase 6 (putative                   function)       1242_at   down   0.023776473   Ets2 repressor factor       40457_at   down   0.023802156   splicing factor, arginine/serine-rich 3       33590_at   up   0.023828936       40555_at   down   0.023877609   ras homolog gene family, member Q       39706_at   down   0.023892621   copine III       31315_at   up   0.023921194   immunoglobulin lambda locus       39941_at   down   0.023929111   RAD50 homolog ( S. cerevisiae )       38649_at   down   0.023932788   KIAA0970 protein       33190_g_at   up   0.023944372   chromosome 10 open reading frame 6       37714_at   up   0.023986452   growth associated protein 43       32243_g_at   up   0.024008044   crystallin, alpha B       41248_at   down   0.024018398   likely ortholog of mouse variant polyadenylation protein CSTF-64       37664_at   up   0.024027194   developmentally regulated GTP binding protein 2       41867_at   up   0.024045128   old astrocyte specifically induced substance       41193_at   down   0.024051364   dual specificity phosphatase 6       35205_at   up   0.02406628   cofactor of BRCA1       40981_at   up   0.024097695   helicase with SNF2 domain 1       38892_at   down   0.024103087   KIAA0240 protein       35363_at   down   0.024128323   DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 17, 72 kDa       36540_at   up   0.024133889   Rho-related BTB domain containing 2       1724_at   up   0.02414433   E2F transcription factor 4, p107/p130-binding       40009_at   up   0.024159688   fragile X mental retardation 2       534_s_at   up   0.02416274   folate receptor 1 (adult)       37723_at   down   0.024176482   cyclin G2       35489_at   up   0.024251424   meprin A, alpha (PABA peptide hydrolase)       227_g_at   down   0.024262631   protein kinase, cAMP-dependent, regulatory, type I, alpha (tissue                   specific extinguisher 1)       1316_at   up   0.024262768   thyroid hormone receptor, alpha (erythroblastic leukemia viral (v-                   erb-a) oncogene homolog, avian)       36018_at   up   0.024269622   SRY (sex determining region Y)-box 10       32728_at   up   0.024280106   amphiphysin (Stiff-Man syndrome with breast cancer 128 kDa                   autoantigen)       1825_at   down   0.024316799   IQ motif containing GTPase activating protein 1       38594_i_at   up   0.024320041   KIAA0284 protein       36014_at   up   0.024334234   G protein-coupled receptor 126       1898_at   up   0.024335806   tripartite motif-containing 29       605_at   up   0.024351877   vesicle amine transport protein 1 homolog ( T californica )       37122_at   up   0.024415515   perilipin       34933_at   up   0.024433571   paired box gene 9       39897_at   down   0.024487745   splicing factor YT521-B       38558_at   up   0.024488796   myelin associated glycoprotein       1072_g_at   up   0.024497847   GATA binding protein 2       37285_at   up   0.024530431   aminolevulinate, delta-, synthase 2 (sideroblastic/hypochromic                   anemia)       33069_f_at   up   0.02458139   UDP glycosyltransferase 2 family, polypeptide B15       36031_at   down   0.024608101   inhibitor of growth family, member 1       37511_at   up   0.02461872   B9 protein       39158_at   up   0.024708448   activating transcription factor 5       39744_at   down   0.024753389   DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3       1658_g_at   up   0.024762036   protein tyrosine phosphatase, receptor type, R       33346_r_at   up   0.024763958   tubulin, gamma 1       33245_at   down   0.024776732   mitogen-activated protein kinase 13       32066_g_at   up   0.024824897   cAMP responsive element modulator       36143_at   down   0.024857059   caspase 3, apoptosis-related cysteine protease       36269_at   up   0.024858179   a disintegrin-like and metalloprotease (reprolysin type) with                   thrombospondin type 1 motif, 3       33071_at   up   0.024871677   histone 1, H2bo       32214_at   down   0.024880537   thioredoxin-like, 32 kDa       39797_at   down   0.024903869   ubiquitin ligase E3 alpha-II       33359_at   up   0.024907251   latrophilin 3       34981_at   up   0.024912595   potassium voltage-gated channel, shaker-related subfamily,                   member 5       41283_at   down   0.02498879   heterogeneous nuclear ribonucleoprotein H3 (2H9)       37134_f_at   up   0.025015777   glutamate receptor, ionotropic, N-methyl D-aspartate 1       35298_at   down   0.02502439   eukaryotic translation initiation factor 3, subunit 7 zeta, 66/67 kDa       39625_at   up   0.025069218       35387_r_at   up   0.025073822   acetylcholinesterase (YT blood group)       31893_at   up   0.025085609   ADP-ribosylation factor-like 2       34305_at   down   0.025125133   poly(rC) binding protein 1       39195_s_at   up   0.025149176   leucine-rich repeats and immunoglobulin-like domains 1       37745_s_at   up   0.025167309   suppression of tumorigenicity 5       39705_at   up   0.025174264   SIN3 homolog B, transcriptional regulator (yeast)       38772_at   up   0.025198255   cysteine-rich, angiogenic inducer, 61       40746_at   up   0.025242905   glutamate receptor, ionotropic, AMPA 2       1482_g_at   up   0.025285618   matrix metalloproteinase 12 (macrophage elastase)       34850_at   down   0.025301859   ubiquitin-conjugating enzyme E2E 3 (UBC4/5 homolog, yeast)       39123_s_at   up   0.025338973   transient receptor potential cation channel, subfamily C, member       186_at   up   0.025376205   protein kinase, AMP-activated, alpha 2 catalytic subunit       40108_at   down   0.025392776   basic leucine zipper and W2 domains 1       39517_at   down   0.025404739   HTGN29 protein       35997_g_at   up   0.025409702   ZW10 interactor anti-sense       37254_at   up   0.025432778   zinc finger protein 133 (clone pHZ-13)       32872_at   up   0.025443671       40988_at   down   0.025483862   YME1-like 1 ( S. cerevisiae )       35813_at   up   0.025524962   transportin-SR       31778_at   up   0.025549358   gap junction protein, alpha 8, 50 kDa (connexin 50)       41652_at   up   0.025591657   collagen, type XI, alpha 2       34805_at   up   0.025620228   hypothetical protein MGC2574       37720_at   down   0.025630855   heat shock 60 kDa protein 1 (chaperonin)       35447_s_at   up   0.025651802   acetylserotonin O-methyltransferase       39172_at   down   0.025654012   hypothetical protein FLJ14547       31995_g_at   up   0.025687138   ADP-ribosylation factor guanine nucleotide-exchange factor 2                   (brefeldin A-inhibited)       36875_at   down   0.02574627   inhibitor of Bruton&#39;s tyrsoine kinase       32301_at   up   0.025789564   guanylate cyclase 1, soluble, alpha 2       35010_at   up   0.025810869   HLA complex group 8       36367_at   up   0.025830383   protocadherin 11 X-linked       37488_at   up   0.02585489   farnesyltransferase, CAAX box, beta       726_f_at   up   0.025905675       31935_s_at   up   0.025909825   DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (CHL1-like                   helicase homolog,  S. cerevisiae )       34819_at   down   0.02591587   CD164 antigen, sialomucin       1449_at   down   0.02591764   proteasome (prosome, macropain) subunit, alpha type, 4       35903_at   up   0.026012105   oligodendrocyte myelin glycoprotein       36890_at   up   0.026034077   periplakin       37794_at   up   0.026039344       34903_at   up   0.026052906   KIAA1218 protein       38215_at   up   0.026063497   chromosome 22 open reading frame 1       160022_at   down   0.026067385   colony stimulating factor 1 receptor, formerly McDonough feline                   sarcoma viral (v-fms) oncogene homolog       31727_at   up   0.026069485   ectonucleoside triphosphate diphosphohydrolase 2       33732_at   up   0.026076534   adaptor-related protein complex 4, mu 1 subunit       35845_at   down   0.026142932   SEC24 related gene family, member B ( S. cerevisiae )       1954_at   up   0.026144402   kinase insert domain receptor (a type III receptor tyrosine kinase)       39820_at   up   0.026155871   RNA polymerase I transcription factor RRN3       1772_s_at   down   0.026179299   farnesyltransferase, CAAX box, alpha       34224_at   up   0.026179949   fatty acid desaturase 3       36445_at   up   0.026189391   chemokine (C—C motif) ligand 23       35614_at   down   0.026217146   transcription factor-like 5 (basic helix-loop-helix)       37558_at   up   0.026217683   IGF-II mRNA-binding protein 3       33172_at   up   0.026290468   hypothetical protein FLJ10849       39877_at   up   0.026319532   potassium voltage-gated channel, Shaw-related subfamily,                   member 4       31922_i_at   up   0.026326432   Ac-like transposable element       40534_at   up   0.026341303   protein tyrosine phosphatase, receptor type, D       1632_at   up   0.026362721       1411_at   up   0.026495528   cytochrome P450, family 11, subfamily B, polypeptide 1       34576_at   up   0.026513529   melanoma antigen, family A, 8       36037_g_at   up   0.026518478   spectrin, beta, erythrocytic (includes spherocytosis, clinical type I)       37736_at   down   0.02652131   protein-L-isoaspartate (D-aspartate) O-methyltransferase       33898_at   up   0.026563809   microspherule protein 1       1243_at   up   0.026567603   damage-specific DNA binding protein 2, 48 kDa       37969_at   up   0.02662293   prostaglandin-endoperoxide synthase 1 (prostaglandin G/H                   synthase and cyclooxygenase)       38967_at   down   0.026666699   chromosome 14 open reading frame 2       34563_at   up   0.026707179   kinesin family member 14       41637_at   up   0.026727557   MYLE protein       33887_at   up   0.026739087   hepatocyte growth factor-regulated tyrosine kinase substrate       36568_at   up   0.026745623   solute carrier family 17 (sodium-dependent inorganic phosphate                   cotransporter), member 7       37470_at   up   0.026754858   leukocyte-associated Ig-like receptor 1       38076_at   up   0.026783134   ATP synthase, H+ transporting, mitochondrial F0 complex, subuni                   c (subunit 9), isoform 1       598_at   up   0.026832268   collagen, type II, alpha 1 (primary osteoarthritis,                   spondyloepiphyseal dysplasia, congenital)       32540_at   up   0.026889206   protein phosphatase 3 (formerly 2B), catalytic subunit, gamma                   isoform (calcineurin A gamma)       34398_at   up   0.026895399   heat shock 105 kDa/110 kDa protein 1       34880_at   down   0.02690197   hypothetical protein MGC10433       41333_at   down   0.02691227   centaurin, beta 2       687_at   up   0.026947578       35150_at   up   0.026964489   tumor necrosis factor receptor superfamily, member 5       36736_f_at   down   0.026980201   phosphoserine phosphatase       31716_at   up   0.026993707   protocadherin 1 (cadherin-like 1)       34294_at   up   0.02707396   kinesin family member C3       32898_at   up   0.027097609   actin like protein       40858_at   up   0.02711133   pregnancy specific beta-1-glycoprotein 1       39740_g_at   down   0.02714561   nascent-polypeptide-associated complex alpha polypeptide       32841_at   down   0.027165304   zinc finger protein 9 (a cellular retroviral nucleic acid binding                   protein)       33253_at   down   0.027189829   tripartite motif-containing 14       38680_at   up   0.027225635   small nuclear ribonucleoprotein polypeptide E       40655_at   up   0.027239968   huntingtin-associated protein interacting protein (duo)       1671_s_at   up   0.027242438   mitogen-activated protein kinase 14       335_r_at   up   0.027250575       31846_at   up   0.02727266   ras homolog gene family, member D       38564_at   up   0.027279452   origin recognition complex, subunit 1-like (yeast)       34926_at   up   0.027289913   CD1A antigen, a polypeptide       39746_at   down   0.027291894   polymerase (RNA) II (DNA directed) polypeptide B, 140 kDa       1041_at   up   0.027299453   ephrin-A5       34159_at   up   0.027348803   RAB7, member RAS oncogene family       39972_at   up   0.027368356   G protein-coupled receptor 17       31831_at   up   0.027395463   smoothelin       31800_at   up   0.027462703       31594_at   up   0.027473933   keratin, hair, acidic, 3A       34154_at   up   0.02749165   cholinergic receptor, nicotinic, beta polypeptide 2 (neuronal)       38048_at   up   0.027500957   RNA binding protein with multiple splicing       1011_s_at   down   0.027503898   tyrosine 3-monooxygenase/tryptophan 5-monooxygenase                   activation protein, epsilon polypeptide       35075_at   up   0.027506345   C18B11 homolog (44.9 kD)       37374_at   down   0.027538074   annexin A4       33719_at   up   0.027545401   synaptopodin       31446_s_at   up   0.027567801   proline rich 5 (salivary)       34537_at   up   0.027593937   potassium inwardly-rectifying channel, subfamily J, member 12       36274_at   up   0.027615478   solute carrier family 7 (cationic amino acid transporter, y+ system)                   member 1       36399_at   up   0.027680522   pre-mRNA splicing SR protein rA4       34823_at   down   0.02770756   dipeptidylpeptidase 4 (CD26, adenosine deaminase complexing                   protein 2)       1558_g_at   down   0.027712082   p21/Cdc42/Rac1-activated kinase 1 (STE20 homolog, yeast)       1661_i_at   up   0.027721213       36715_at   up   0.02776357   adrenergic, alpha-1A-, receptor       39572_at   up   0.027785371   glutamate receptor, ionotropic, kainate 2       38016_at   down   0.027802172   heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA                   binding protein 1, 37 kDa)       38077_at   up   0.027810469   collagen, type VI, alpha 3       40557_at   up   0.02789479   guanylate cyclase activator 1B (retina)       34486_at   up   0.027907141       39573_at   up   0.027923396   glutamate receptor, ionotropic, kainate 2       37780_at   up   0.027968479   piccolo (presynaptic cytomatrix protein)       32019_at   up   0.02799539   DKFZP434C153 protein       31522_f_at   up   0.028090065   histone 1, H2bf       685_f_at   down   0.028154459   tubulin, alpha 1 (testis specific)       37840_at   up   0.02820166   cyclic nucleotide gated channel alpha 1       40146_at   down   0.028209265   RAP1B, member of RAS oncogene family       41002_at   up   0.028243866   solute carrier family 16 (monocarboxylic acid transporters),                   member 5       32012_at   up   0.028268131   pecanex homolog ( Drosophila )       31984_at   up   0.028270556       41294_at   up   0.02828124   keratin 7       41633_at   up   0.028282157   sentrin/SUMO-specific protease 3       32184_at   down   0.028317805   LIM domain only 2 (rhombotin-like 1)       40913_at   down   0.028333047   ATPase, Ca++ transporting, plasma membrane 4       33996_at   up   0.028357358   neuromedin B receptor       34640_at   up   0.028368648   transcription factor 1, hepatic; LF-B1, hepatic nuclear factor                   (HNF1), albumin proximal factor       38962_at   up   0.028378275   KIAA0298 gene product       37157_at   up   0.028380947   calbindin 2, 29 kDa (calretinin)       2028_s_at   up   0.028383411   E2F transcription factor 1       38198_at   up   0.028391962   similar to RIKEN cDNA 2610307I21       1659_s_at   down   0.028544189   Ras homolog enriched in brain 2       38729_at   up   0.028553044   FK506 binding protein 4, 59 kDa       33950_g_at   up   0.028656928   corticotropin releasing hormone receptor 2       41555_at   up   0.028666961   heparan sulfate (glucosamine) 3-O-sulfotransferase 1       32946_r_at   up   0.028673572   mannose-binding lectin (protein C) 2, soluble (opsonic defect)       36981_at   down   0.028721449   signal recognition particle 9 kDa       31500_at   up   0.028739978   N-myc downstream regulated gene 1       105_at   up   0.028747273   nuclear receptor subfamily 1, group I, member 3       37369_s_at   up   0.028795072   nuclear factor of activated T-cells, cytoplasmic, calcineurin-                   dependent 4       1900_at   up   0.028796398   retinoblastoma 1 (including osteosarcoma)       37358_at   down   0.028871178   ubiquitin-conjugating enzyme E2E 1 (UBC4/5 homolog, yeast)       1062_g_at   down   0.028894304   interleukin 10 receptor, alpha       247_s_at   up   0.028908676   cytochrome P450, family 21, subfamily A, polypeptide 2       33184_at   up   0.028926665   guanylate cyclase activator 1A (retina)       40144_at   down   0.028926721   protein tyrosine phosphatase, non-receptor type substrate 1       1902_at   up   0.028929735   excision repair cross-complementing rodent repair deficiency,                   complementation group 1 (includes overlapping antisense                   sequence)       237_s_at   down   0.02901457   protein phosphatase 2 (formerly 2A), catalytic subunit, alpha                   isoform       32871_at   up   0.029039566       40129_at   down   0.029043392   protein kinase, DNA-activated, catalytic polypeptide       33852_at   down   0.029046277   TIA1 cytotoxic granule-associated RNA binding protein       41190_at   up   0.029048795   tumor necrosis factor receptor superfamily, member 25       34505_at   up   0.029085088   likely ortholog of mouse myocytic induction/differentiation                   originator       39911_at   up   0.029122116   hypothetical protein LOC51257       34334_at   up   0.029129367   ephrin-B2       32819_at   down   0.029198273   histone 1, H2bk       40012_at   up   0.02922851   low density lipoprotein receptor-related protein 8, apolipoprotein e                   receptor       1505_at   up   0.029239491   thymidylate synthetase       35814_at   down   0.029305093   dendritic cell protein       39955_at   up   0.029314355   deleted in lymphocytic leukemia, 2       37989_at   up   0.029335797   parathyroid hormone-like hormone       33416_at   up   0.029369792   KIAA1049 protein       41678_at   up   0.029375379   EphB2       41757_at   down   0.029390472   VAMP (vesicle-associated membrane protein)-associated protein                   B and C       35981_at   up   0.029401129   regenerating islet-derived 1 beta (pancreatic stone protein,                   pancreatic thread protein)       32534_f_at   up   0.029407674   vesicle-associated membrane protein 5 (myobrevin)       716_at   up   0.029510223   gamma-glutamyltransferase-like activity 1       41336_at   up   0.029552307   DKFZP566O1646 protein       34774_at   down   0.029555309   palmitoyl-protein thioesterase 1 (ceroid-lipofuscinosis, neuronal 1,                   infantile)       1784_s_at   down   0.029583432   retinoblastoma binding protein 1       1517_at   up   0.029610936   cytochrome P450, family 2, subfamily F, polypeptide 1       40700_at   up   0.029668614   SP140 nuclear body protein       40323_at   up   0.029749549   CD38 antigen (p45)       37238_s_at   up   0.029796885   membrane-associated tyrosine- and threonine-specific cdc2-                   Inhibitory kinase       2086_s_at   up   0.029837041   TYRO3 protein tyrosine kinase       34351_at   up   0.029891028   phospholipase C, gamma 1 (formerly subtype 148)       467_at   down   0.029903899   osteoclast stimulating factor 1       35571_at   up   0.029924365   coagulation factor II (thrombin) receptor-like 3       33965_at   up   0.029960532   chemokine (C—C motif) ligand 1       41696_at   up   0.029980756   hypothetical protein MGC3077       36285_at   up   0.030018837   potassium inwardly-rectifying channel, subfamily J, member 4       322_at   up   0.030077773   phosphoinositide-3-kinase, regulatory subunit, polypeptide 3 (p55                   gamma)       38498_at   up   0.030096154   crystallin, beta B2       40836_s_at   up   0.030118354   heterogeneous nuclear ribonucleoprotein H3 (2H9)       232_at   up   0.030119073   laminin, gamma 1 (formerly LAMB2)       39174_at   down   0.030122401   nuclear receptor coactivator 4       37755_at   up   0.0301373   BTB (POZ) domain containing 3       39967_at   up   0.030138107   leucine zipper, down-regulated in cancer 1       38897_at   up   0.030160347   solute carrier family 7 (cationic amino acid transporter, y+ system                   member 4       2050_s_at   down   0.030191058   ras-related C3 botulinum toxin substrate 1 (rho family, small GTP                   binding protein Rac1)       35020_at   up   0.030204148   paired-like homeobox 2b       32505_at   up   0.030207295   NS1-associated protein 1       33302_at   up   0.030208659   sarcospan (Kras oncogene-associated gene)       33799_at   down   0.030209223   seven in absentia homolog 2 ( Drosophila )       40840_at   up   0.03025459   peptidylprolyl isomerase F (cyclophilin F)       191_at   up   0.030325967   mucin 8, tracheobronchial       35090_g_at   up   0.030333092   neuregulin 2       40068_at   down   0.030347738   syntaxin 5A       39049_at   down   0.030357581   chromosome 6 open reading frame 9       34067_at   up   0.030369064       35930_at   up   0.030372209   testis specific protein, Y-linked       33459_at   up   0.03040696       37418_at   up   0.030409086   POU domain, class 2, transcription factor 2       34149_at   up   0.030409172   pleiotropic regulator 1 (PRL1homolog,  Arabidopsis )       41085_at   up   0.030435923   polymerase (DNA directed), epsilon 2 (p59 subunit)       40783_s_at   up   0.030449434   phosphatidylinositol 4-kinase, catalytic, alpha polypeptide       892_at   up   0.030460619   transmembrane 4 superfamily member 1       40203_at   down   0.030488383   putative translation initiation factor       32002_at   up   0.030532859   GDNF family receptor alpha 3       37463_r_at   up   0.030546476   splicing factor 3a, subunit 2, 66 kDa       38714_at   up   0.03055242   glycophorin A (includes MN blood group)       34726_at   up   0.030570264   calcium channel, voltage-dependent, beta 3 subunit       41374_at   up   0.030608379   ribosomal protein S6 kinase, 70 kDa, polypeptide 2       36023_at   down   0.030629492   proline-rich protein HaeIII subfamily 1       36742_at   up   0.030653119   tripartite motif-containing 15       36771_at   up   0.030722552   cannabinoid receptor 2 (macrophage)       159_at   up   0.030730643   vascular endothelial growth factor C       AFFX-CreX-5_at   up   0.030730678       39429_at   up   0.030749245   UV radiation resistance associated gene       34463_at   up   0.030750243   deoxyribonuclease I       824_at   down   0.030756422   glutathione-S-transferase like; glutathione transferase omega       35593_at   up   0.030776042   amine oxidase, copper containing 2 (retina-specific)       1090_f_at   up   0.030790531   vacuolar protein sorting 4B (yeast)       33576_at   up   0.03087025   KIAA0918 protein       923_at   up   0.030878031   ubiquitin-like 4       39607_at   up   0.030920096   myotubularin related protein 9       34554_at   up   0.030941865   glycine receptor, alpha 2       1858_at   up   0.030996193   tumor necrosis factor (ligand) superfamily, member 6       36433_at   up   0.031004583   glycine receptor, alpha 3       1427_g_at   down   0.031021674   Src-like-adaptor       634_at   up   0.031040949   protease, serine, 8 (prostasin)       32700_at   down   0.031048619   guanylate binding protein 2, interferon-inducible       38492_at   up   0.031061258   kynureninase (L-kynurenine hydrolase)       34127_at   up   0.031061577   organic cationic transporter-like 3       1153_f_at   up   0.031069865   chorionic gonadotropin, beta polypeptide       35102_at   up   0.031116602   zinc finger protein       35325_at   down   0.031161778   RAB14, member RAS oncogene family       35638_at   up   0.031168273   core-binding factor, runt domain, alpha subunit 2; translocated to,                   1; cyclin D-related       37389_at   down   0.031316111   small acidic protein       31961_r_at   up   0.031323988       36439_at   up   0.031332099       32254_at   up   0.031358273   vesicle-associated membrane protein 2 (synaptobrevin 2)       36701_at   up   0.03135917       1628_at   up   0.031360464       37397_at   down   0.031394119   platelet/endothelial cell adhesion molecule (CD31 antigen)       39420_at   down   0.031398275   DNA-damage-inducible transcript 3       32228_at   up   0.031413344   adaptor-related protein complex 2, alpha 2 subunit       32053_at   down   0.031474283   cyclin T2       36509_at   down   0.031476516   ribosomal protein L35a       36793_at   up   0.03149691   hypothetical protein AY099107       31941_s_at   up   0.031534979   ret finger protein-like 3       33999_f_at   up   0.031557766       34924_at   up   0.031605825   kinesin family member 1B       37850_at   up   0.031616361   hypothetical protein dJ462O23.2       1853_at   up   0.031673028   wingless-type MMTV integration site family, member 1       32761_at   up   0.031711267   serine/arginine repetitive matrix 2       35848_at   down   0.031713305   retinoic acid induced 17       33058_at   up   0.03184771   cytokeratin type II       635_s_at   up   0.031851567   protein phosphatase 2, regulatory subunit B (B56), beta isoform       35411_at   up   0.031857375   chromosome 16 open reading frame 7       32520_at   up   0.031885468   nuclear receptor subfamily 1, group D, member 1       31915_at   up   0.031889645   dystrophin related protein 2       36714_at   up   0.031890786   nuclear receptor subfamily 2, group C, member 2       34847_s_at   up   0.031912545   calcium/calmodulin-dependent protein kinase (CaM kinase) II beta       424_s_at   up   0.031967116   fibroblast growth factor receptor 1 (fms-related tyrosine kinase 2,                   Pfeiffer syndrome)       31414_at   up   0.031975481   testis-specific transcript, Y-linked 2       32896_at   up   0.032009199       35417_at   up   0.03208939   cubilin (intrinsic factor-cobalamin receptor)       35263_at   down   0.032117131   eukaryotic translation initiation factor 4E binding protein 2       1573_at   up   0.032134508   platelet-derived growth factor beta polypeptide (simian sarcoma                   viral (v-sis) oncogene homolog)       792_s_at   up   0.032185586   transcription factor AP-2 alpha (activating enhancer binding                   protein 2 alpha)       33232_at   down   0.032194657   cysteine-rich protein 1 (intestinal)       37545_at   up   0.032225183   secretory carrier membrane protein 5       41630_at   up   0.032231183   CGI-62 protein       35285_at   up   0.032272611   solute carrier family 4, sodium bicarbonate cotransporter, member 4       41618_at   up   0.032282842   collagen, type XVII, alpha 1       39497_at   up   0.032294796   hypothetical protein FLJ10803       41324_g_at   up   0.032328237   forkhead box M1       36716_at   up   0.032332777   adrenergic, alpha-1A-, receptor       38191_at   up   0.032337124   KIAA0645 gene product       36315_i_at   up   0.032376572   Sec15B protein       34128_at   up   0.032402682   UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5       33356_at   up   0.032468294   trinucleotide repeat containing 3       31566_at   up   0.032480202       37811_at   up   0.032501096   calcium channel, voltage-dependent, alpha 2/delta subunit 2       37035_at   down   0.03252466   stress-associated endoplasmic reticulum protein 1       37165_f_at   up   0.032565127   Rhesus blood group, CcEe antigens       32499_at   up   0.032569682   Rho GDP dissociation inhibitor (GDI) gamma       36200_at   up   0.032605501   HLA-B associated transcript 8       31443_at   up   0.032611589       38664_at   down   0.032630779   craniofacial development protein 1       423_at   down   0.0326721   Ewing sarcoma breakpoint region 1       39206_s_at   up   0.032698078   aggrecan 1 (chondroitin sulfate proteoglycan 1, large aggregating                   proteoglycan, antigen identified by monoclonal antibody A0122)       41467_at   up   0.032750937   mutS homolog 5 ( E. coli )       38755_at   up   0.032752728   Fas (TNFRSF6)-associated via death domain       34575_f_at   up   0.032809836   melanoma antigen, family A, 5       35553_at   up   0.032825078   TSPY-like       38221_at   up   0.032832296   connector enhancer of KSR-like ( Drosophila  kinase suppressor o                   ras)       35362_at   up   0.03290105   myosin X       35400_at   up   0.032907138       221_s_at   up   0.032936681   phosphatidylinositol glycan, class A (paroxysmal nocturnal                   hemoglobinuria)       36093_at   up   0.032947133   KIAA0614 protein       36462_at   up   0.032953356   SMYD family member 5       1892_s_at   up   0.032967779       38766_at   up   0.033003801   Snf2-related CBP activator protein       39276_g_at   up   0.033018192   calcium channel, voltage-dependent, L type, alpha 1D subunit       37922_at   up   0.033026389   transcobalamin II; macrocytic anemia       38390_at   up   0.033060083   component of oligomeric golgi complex 2       40916_at   down   0.033066997   hypothetical protein FLJ10097       36094_at   up   0.033067781   troponin T3, skeletal, fast       35184_at   down   0.033082679   KIAA0546 protein       35537_at   up   0.033137937   tumor necrosis factor receptor superfamily, member 10d, decoy                   with truncated death domain       40759_at   up   0.03313989   matrix metalloproteinase 16 (membrane-inserted)       38084_at   down   0.033140959   chromobox homolog 3 (HP1 gamma homolog,  Drosophila )       38934_at   up   0.033155647       35995_at   up   0.033159596   ZW10 interactor       39000_at   up   0.033222247   N-myristoyltransferase 1       31791_at   up   0.033224619   tumor protein p73-like       31392_r_at   up   0.033262168   chromosome 1 open reading frame 1       36248_at   up   0.033265588   NAG-5 protein       35564_at   up   0.033280281       223_at   down   0.033309012   ubiquitin-conjugating enzyme E2L 3       37781_at   up   0.033368336   neurexin 2       40295_at   up   0.033391699   copine VI (neuronal)       35191_at   up   0.033424161   KIAA0375 gene product       171_at   down   0.033442103   von Hippel-Lindau binding protein 1       39046_at   down   0.033467681   histone H2A.F/Z variant       36369_at   up   0.033478368   polymerase I and transcript release factor       1789_at   down   0.033529093   COP9 constitutive photomorphogenic homolog subunit 5                   ( Arabidopsis )       33121_g_at   down   0.033549364   regulator of G-protein signalling 10       32659_at   down   0.033576868   eukaryotic translation initiation factor 2B, subunit 4 delta, 67 kDa       37234_at   up   0.033609251   kininogen       457_s_at   down   0.033618854   ubiquitin-like 1 (sentrin)       34173_s_at   up   0.033652359   contactin 5       34604_at   up   0.0336552   solute carrier family 6 (neurotransmitter transporter, serotonin),                   member 4       1155_at   up   0.033705413   v-myc myelocytomatosis viral oncogene homolog 2 (avian)       35316_at   down   0.033716548   Ras-related GTP-binding protein       34355_at   down   0.033779716   methyl CpG binding protein 2 (Rett syndrome)       1156_at   up   0.033793231   Sp1 transcription factor       36516_at   up   0.033803067   zinc finger protein ZFP100       31321_at   up   0.033837372   pancreatic beta cell growth factor       40097_at   down   0.033852776   eukaryotic translation initiation factor 1A, Y chromosome       33839_at   up   0.033863607   inositol 1,4,5-triphosphate receptor, type 2       34626_at   up   0.033878835   hypermethylated in cancer 1       326_i_at   down   0.03389412       40239_g_at   up   0.033906971   G protein-coupled receptor, family C, group 5, member B       34722_at   up   0.033910912   tissue inhibitor of metalloproteinase 2       35454_at   up   0.033944357   KIAA0450 gene product       1613_s_at   up   0.033952839   ubiquitin specific protease 6 (Tre-2 oncogene)       35693_at   up   0.033996591   hippocalcin-like 1       1095_s_at   up   0.034001673   hepatocyte growth factor (hepapoietin A; scatter factor)       41573_at   down   0.034024859   Sp3 transcription factor       33677_at   down   0.034077303   ribosomal protein L24       41388_at   up   0.03408507   Meis1, myeloid ecotropic viral integration site 1 homolog 2                   (mouse)       32409_at   up   0.034121256   phosphatidylinositol glycan class O       37788_at   up   0.03412756       38980_at   down   0.034131969   mitogen-activated protein kinase kinase kinase 7 interacting                   protein 2       34897_at   up   0.034163537   protein phosphatase 4, regulatory subunit 2       32221_at   down   0.034177991   mitochondrial ribosomal protein S18B       38323_at   down   0.034293103   carboxypeptidase, vitellogenic-like       33570_at   up   0.034304188   NK2 transcription factor related, locus 5 ( Drosophila )       36318_at   up   0.034313433   homolog of rat orphan transporter v7-3       35967_at   up   0.034376104   aryl hydrocarbon receptor nuclear translocator       31659_at   up   0.034390954   DKFZP434K091 protein       31661_at   up   0.034425691       41756_at   down   0.034438173   XPA binding protein 1       33046_f_at   up   0.034440875   empty spiracles homolog 1 ( Drosophila )       37666_at   up   0.034522353   proteasome (prosome, macropain) subunit, beta type, 5       32425_at   up   0.034526343   cholinergic receptor, nicotinic, alpha polypeptide 2 (neuronal)       40571_at   down   0.03453232   myosin VA (heavy polypeptide 12, myoxin)       33219_at   down   0.034561079   pVHL-interacting deubiquitinating enzyme 1       32267_at   up   0.034563899   zinc finger protein 345       31510_s_at   down   0.034573927   H3 histone, family 3B (H3.3B)       39652_at   up   0.034588394   chemokine (C motif) ligand 1       1782_s_at   up   0.034594134   stathmin 1/oncoprotein 18       38819_at   up   0.034640515   PTK7 protein tyrosine kinase 7       39221_at   down   0.034659495   leukocyte immunoglobulin-like receptor, subfamily B (with TM and                   ITIM domains), member 2       37813_at   up   0.034669603       38056_at   up   0.034690705   KIAA0195 gene product       527_at   up   0.034691647   centromere protein A, 17 kDa       33137_at   up   0.034815653   latent transforming growth factor beta binding protein 4       34743_at   up   0.03491869   scribble       40954_at   up   0.034930625   FXYD domain containing ion transport regulator 2       32739_at   up   0.034938417   phosphoglucomutase 3       39747_at   down   0.034979203   polymerase (RNA) II (DNA directed) polypeptide G       40672_at   up   0.035009921   kynureninase (L-kynurenine hydrolase)       34607_at   up   0.0350146   inducible T-cell co-stimulator       32991_f_at   up   0.035068269   amelogenin (Y chromosome)       31314_at   up   0.035072962   bone morphogenetic protein 3 (osteogenic)       33178_at   up   0.035088856   jagged 1 (Alagille syndrome)       37832_at   up   0.035109738   DKFZP564I122 protein       802_at   down   0.035128062   TAF12 RNA polymerase II, TATA box binding protein (TBP)-                   associated factor, 20 kDa       32025_at   down   0.035193294   transcription factor 7-like 2 (T-cell specific, HMG-box)       39086_g_at   down   0.035197215   single-stranded DNA binding protein       39777_at   down   0.035201873   protein associated with Myc       35260_at   up   0.03524273   Mix interactor       33247_at   down   0.03528389   proteasome (prosome, macropain) 26S subunit, non-ATPase, 14       39179_at   up   0.035361402   proteoglycan 2, bone marrow (natural killer cell activator,                   eosinophil granule major basic protein)       35038_at   up   0.035365152   myosin binding protein C, cardiac       35742_at   up   0.0353725   hypothetical gene BC008967       38308_g_at   up   0.035420841   neurochondrin       37177_at   down   0.035452242   CD58 antigen, (lymphocyte function-associated antigen 3)       38066_at   up   0.035462531   NAD(P)H dehydrogenase, quinone 1       38528_at   up   0.035497003   acetyl-Coenzyme A carboxylase alpha       32248_at   down   0.035497896   hypothetical protein PRO2730       32548_at   down   0.035500275   unactive progesterone receptor, 23 kD       32263_at   up   0.035509211   cyclin B2       32622_at   up   0.03554138   dynamin 2       35327_at   down   0.03561689   eukaryotic translation initiation factor 3, subunit 3 gamma, 40 kDa       37001_at   down   0.035620522   calpain 2, (m/II) large subunit       35207_at   up   0.035647227   sodium channel, nonvoltage-gated 1 alpha       37697_s_at   down   0.035661664   voltage-dependent anion channel 2       34637_f_at   up   0.035677011   alcohol dehydrogenase 1A (class I), alpha polypeptide       40238_at   up   0.035681038   G protein-coupled receptor, family C, group 5, member B       41657_at   up   0.035748093   serine/threonine kinase 11 (Peutz-Jeghers syndrome)       38072_at   down   0.035800174   hypothetical protein dJ465N24.2.1       35949_at   up   0.035817369   KIAA0774 protein       39133_at   down   0.035822484   GCN5 general control of amino-acid synthesis 5-like 1 (yeast)       440_at   up   0.035839885   nuclear factor I/C (CCAAT-binding transcription factor)       39032_at   down   0.035842888   transforming growth factor beta-stimulated protein TSC-22       36859_at   up   0.03584934   non-metastatic cells 5, protein expressed in (nucleoside-                   diphosphate kinase)       32075_at   up   0.035852074   zinc finger protein 161 homolog (mouse)       41007_at   up   0.03590906   myozenin 3       37908_at   down   0.035935871   guanine nucleotide binding protein (G protein), gamma 11       39111_s_at   down   0.035951483   peptidylprolyl isomerase (cyclophilin)-like 2       39390_at   down   0.035991974   nucleoporin 133 kDa       1536_at   up   0.036029396   CDC6 cell division cycle 6 homolog ( S. cerevisiae )       40810_at   down   0.036034327   SWI/SNF related, matrix associated, actin dependent regulator of                   chromatin, subfamily c, member 1       39015_f_at   up   0.036068618   keratin 6A       31439_f_at   up   0.036084452   Rhesus blood group, CcEe antigens       38291_at   up   0.036104104   proenkephalin       39217_at   up   0.036118403       728_at   up   0.03612594       40267_s_at   up   0.036136261   KIAA1036 protein       35442_at   up   0.036186437   KIAA0792 gene product       39034_at   down   0.036243812   DKFZP564O123 protein       33227_at   down   0.036245055   interleukin 10 receptor, beta       39927_at   up   0.036258257   Rho GTPase activating protein 5       31365_f_at   up   0.036274538   nuclear factor of activated T-cells 5, tonicity-responsive       883_s_at   up   0.036301176   pim-1 oncogene       1512_at   down   0.036307971   dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A       35011_at   down   0.036313265   HECT type E3 ubiquitin ligase       38204_at   up   0.036318873   KIAA0406 gene product       37381_g_at   down   0.036360287   general transcription factor IIB       162_at   up   0.036372555   ubiquitin specific protease 11       34568_at   up   0.036382821   keratin, hair, acidic, 3B       34160_at   down   0.036395515   actin, gamma 1       41872_at   up   0.036421973   deafness, autosomal dominant 5       40636_at   up   0.036435919   flotillin 1       1382_at   down   0.036530269   replication protein A1, 70 kDa       36360_at   up   0.036567094   KIAA0507 protein       39542_at   up   0.036640558   ectodermal-neural cortex (with BTB-like domain)       1765_at   up   0.036649057   caspase 10, apoptosis-related cysteine protease       837_s_at   down   0.03665956   malic enzyme 1, NADP(+)-dependent, cytosolic       1949_at   up   0.036688112   angiopoietin 1       37135_f_at   up   0.036721619   glutamate receptor, ionotropic, N-methyl D-aspartate 1       40754_at   up   0.036753843   general transcription factor IIH, polypeptide 3, 34 kDa       39288_at   up   0.036831137   nectin-like protein 1       33580_r_at   up   0.036856676   galanin receptor 3       990_at   up   0.036936172   fms-related tyrosine kinase 1 (vascular endothelial growth                   factor/vascular permeability factor receptor)       41780_at   down   0.036941323   protein tyrosine phosphatase, receptor type, f polypeptide                   (PTPRF), interacting protein (liprin), alpha 1       31412_at   up   0.036983521   PTPN13-like, Y-linked       38544_at   up   0.036991342   inhibin, alpha       39760_at   down   0.036998817   quaking homolog, KH domain RNA binding (mouse)       160026_at   up   0.037003493   protein kinase, X-linked       37844_at   down   0.037057085   class I cytokine receptor       38627_at   up   0.037109589   hepatic leukemia factor       AFFX-M27830_3_at   up   0.037136535       39601_at   up   0.037182176   Ras association (RalGDS/AF-6) domain family 1       39212_at   up   0.037250199   hypothetical protein FLJ11191       35451_s_at   up   0.037307942   SCAN domain containing 2       34064_s_at   up   0.037309471   natural cytotoxicity triggering receptor 2       36956_at   up   0.037350527   solute carrier family 20 (phosphate transporter), member 2       41355_at   down   0.037373862   B-cell CLL/lymphoma 11A (zinc finger protein)       39208_i_at   down   0.037381904   pro-platelet basic protein (chemokine (C—X—C motif) ligand 7)       38415_at   down   0.037413264   protein tyrosine phosphatase type IVA, member 2       38445_at   up   0.037433428   actin related protein 2/3 complex, subunit 2, 34 kDa       1322_at   up   0.037477325       38466_at   up   0.037501653   cathepsin K (pycnodysostosis)       36779_at   up   0.037509117   fatty acid binding protein 6, ileal (gastrotropin)       1295_at   down   0.037566519   v-rel reticuloendotheliosis viral oncogene homolog A, nuclear                   factor of kappa light polypeptide gene enhancer in B-cells 3, p65                   (avian)       37423_at   up   0.037568568   solute carrier family 12 (sodium/potassium/chloride transporters),                   member 2       41406_at   down   0.037620194   hypothetical protein FLJ21919       34112_r_at   up   0.037686408       34038_at   up   0.037720153   solute carrier family 6 (neurotransmitter transporter, GABA),                   member 13       38781_at   up   0.037740959   glutathione S-transferase A2       33045_r_at   up   0.037754364   empty spiracles homolog 1 ( Drosophila )       33420_g_at   down   0.037813208   apoptosis inhibitor 5       34877_at   down   0.037874468   Janus kinase 1 (a protein tyrosine kinase)       39920_r_at   up   0.037908818   C1q-related factor       40617_at   down   0.037913324   hypothetical protein FLJ20274       31602_at   up   0.037939657   T-box 6       39190_s_at   up   0.03794319       38158_at   up   0.037955678   extra spindle poles like 1 ( S. cerevisiae )       39563_at   up   0.037962522   KIAA0268 protein       38393_at   down   0.037967247   KIAA0247 gene product       37986_at   down   0.038002259   erythropoietin receptor       33293_at   up   0.038041132   Fas apoptotic inhibitory molecule 2       35146_at   up   0.0380469   transforming growth factor beta 1 induced transcript 1       34566_at   up   0.038085141   calcitonin-related polypeptide, beta       41246_at   up   0.038116844   serine (or cysteine) proteinase inhibitor, clade E (nexin,                   plasminogen activator inhibitor type 1), member 2       39426_at   down   0.03813583   transcription elongation regulator 1 (CA150)       39608_at   up   0.038173191   single-minded homolog 2 ( Drosophila )       41858_at   up   0.038174864   FGF receptor activating protein 1       37668_at   down   0.038273197   complement component 1, q subcomponent binding protein       35947_at   up   0.038343221   transglutaminase 1 (K polypeptide epidermal type I, protein-                   glutamine-gamma-glutamyltransferase)       41129_at   down   0.038356011   KIAA0033 protein       40268_at   up   0.038387842   FOS-like antigen 2       36617_at   up   0.038390439   inhibitor of DNA binding 1, dominant negative helix-loop-helix                   protein       39946_at   up   0.038392089   pancreatitis-associated protein       35297_at   down   0.038407506   NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1,                   8 kDa       41172_at   down   0.038407527   retinol dehydrogenase 11 (all-trans and 9-cis)       32980_f_at   down   0.038440496   histone 1, H2bc       39364_s_at   up   0.038449579   protein phosphatase 1, regulatory (inhibitor) subunit 3C       33060_g_at   up   0.038481349       39109_at   up   0.038509158   chromosome 20 open reading frame 1       2041_i_at   up   0.038513823   v-abl Abelson murine leukemia viral oncogene homolog 1       37984_s_at   down   0.038552881   ADP-ribosylation factor 6       36746_s_at   up   0.038564507   calcitonin receptor       39616_at   up   0.038593624       1270_at   up   0.038616745   RAP1, GTPase activating protein 1       35464_at   up   0.038622074   interleukin 11       41187_at   down   0.038647669   myosin regulatory light chain MRLC2       39143_at   down   0.038679527   nuclear factor of activated T-cells, cytoplasmic, calcineurin-                   dependent 1       34260_at   up   0.038707405   KIAA0683 gene product       37567_at   up   0.038711751   sal-like 2 ( Drosophila )       35612_at   up   0.038714873   DKFZP564P1916 protein       37858_at   up   0.038730644   collagen-like tail subunit (single strand of homotrimer) of                   asymmetric acetylcholinesterase       34984_at   up   0.038737233   transient receptor potential cation channel, subfamily C, member       33949_at   up   0.03874733   corticotropin releasing hormone receptor 2       342_at   up   0.038767213   ectonucleotide pyrophosphatase/phosphodiesterase 1       33052_at   up   0.038797008   phospholipase A2, group X       41423_at   up   0.038802753   calsyntenin 3       37112_at   down   0.038914634   chromosome 6 open reading frame 32       1754_at   up   0.038967239   death-associated protein 6       33025_at   up   0.038968578   chromosome 20 open reading frame 10       627_g_at   up   0.039082   arginine vasopressin receptor 1B       34731_at   down   0.039093403   programmed cell death 11       32568_at   up   0.039115444   BTG family, member 3       36881_at   down   0.039125362   electron-transfer-flavoprotein, beta polypeptide       41686_s_at   up   0.039157522   NY-REN-7 antigen       38487_at   up   0.039168582   stabilin 1       40417_at   down   0.039177693   chaperonin containing TCP1, subunit 5 (epsilon)       35849_at   up   0.039215248   phosphatidylserine receptor       33243_at   down   0.039241844   TNF-induced protein       32346_at   up   0.039243412       40461_at   up   0.039253806   triple homeobox 1       40028_at   up   0.039264393   LOC92346       34932_at   up   0.039274406   melanoma antigen, family C, 1       37648_at   up   0.039293338   KIAA0153 protein       32542_at   down   0.039325252   four and a half LIM domains 1       39209_r_at   down   0.039349881   pro-platelet basic protein (chemokine (C—X—C motif) ligand 7)       41819_at   down   0.039389573   FYN binding protein (FYB-120/130)       31492_at   down   0.039426982   muscle specific gene       38481_at   down   0.039431725   replication protein A1, 70 kDa       36004_at   up   0.039498058   inhibitor of kappa light polypeptide gene enhancer in B-cells,                   kinase gamma       31551_at   up   0.039538216   gamma-aminobutyric acid (GABA) receptor, rho 2       40613_at   down   0.039628778   chromosome 6 open reading frame 62       37970_at   up   0.039662257   mitogen-activated protein kinase 8 interacting protein 3       1666_at   up   0.039665359   interferon, alpha 1       115_at   down   0.039688446   thrombospondin 1       2037_s_at   up   0.039733454   ribosomal protein S6 kinase, 70 kDa, polypeptide 1       38152_at   up   0.039735408   loss of heterozygosity, 11, chromosomal region 2, gene A       36169_at   down   0.039738748   NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 1,                   7.5 kDa       AFFX-BioB-3_at   up   0.039745177       40353_at   up   0.039779913       31409_at   up   0.039789728   serine (or cysteine) proteinase inhibitor, clade B (ovalbumin),                   member 10       37049_g_at   up   0.039808882   translocase of outer mitochondrial membrane 34       36473_at   up   0.039827121   ubiquitin specific protease 20       35743_at   up   0.039844257   cleavage and polyadenylation specific factor 4, 30 kDa       38444_at   up   0.039897913   cysteine and glycine-rich protein 3 (cardiac LIM protein)       32557_at   up   0.039917401   U2 small nuclear ribonucleoprotein auxiliary factor (65 kD)       34539_at   up   0.039968141   olfactory receptor, family 7, subfamily A, member 126 pseudogene       36851_g_at   up   0.040105766   Putative prostate cancer tumor suppressor       32648_at   up   0.040119322   delta-like 1 homolog ( Drosophila )       39030_at   up   0.040121358   Rab acceptor 1 (prenylated)       39391_at   down   0.04013934   associated molecule with the SH3 domain of STAM       41822_at   up   0.040160905   zinc finger protein       32818_at   up   0.040201801   tenascin C (hexabrachion)       39313_at   up   0.040229309   protein kinase, lysine deficient 1       37926_at   up   0.040231459   Kruppel-like factor 5 (intestinal)       875_g_at   up   0.040259866   chemokine (C—C motif) ligand 2       31487_at   up   0.040270313   fasciculation and elongation protein zeta 2 (zygin II)       38613_at   up   0.040286427   putative cyclin G1 interacting protein       2007_g_at   up   0.040353971   Janus kinase 3 (a protein tyrosine kinase, leukocyte)       39136_at   down   0.040366437   oxidative-stress responsive 1       41782_g_at   up   0.0403846   protein tyrosine phosphatase, receptor type, f polypeptide                   (PTPRF), interacting protein (liprin), alpha 1       35749_at   up   0.040386806   transcriptional adaptor 3 (NGG1 homolog, yeast)-like       39331_at   up   0.040419286   tubulin, beta polypeptide       36476_at   down   0.040425881   bromodomain containing 8       40247_at   up   0.040437893   solute carrier family 9 (sodium/hydrogen exchanger), isoform 7       40167_s_at   down   0.040463083   likely ortholog of mouse WD-40-repeat-containing protein with a                   SOCS box 2       32034_at   down   0.040506981   zinc finger protein 217       40567_at   down   0.040518867   tubulin, alpha 3       40691_at   down   0.040548176   zinc finger protein 274       37005_at   up   0.040561003   neuroblastoma, suppression of tumorigenicity 1       40371_at   up   0.040591204   dopamine receptor D2       31388_at   up   0.040627727   early lymphoid activation protein       AFFX-CreX-3_at   up   0.040647806       41499_at   up   0.040698611   v-ski sarcoma viral oncogene homolog (avian)       38131_at   up   0.040768509   prostaglandin E synthase       40266_at   up   0.04078716   KIAA1036 protein       39324_at   up   0.040788061       1154_at   up   0.040819001   eukaryotic translation initiation factor 2, subunit 1 alpha, 35 kDa       413_at   up   0.040842837   homeo box D9       34299_at   down   0.040881701   zinc finger protein 278       39050_at   up   0.040889932   poly(A) binding protein, nuclear 1       35408_i_at   down   0.040944508   zinc finger protein 44 (KOX 7)       41720_r_at   up   0.040965049   fatty acid desaturase 1       1392_at   up   0.041028012   G protein-coupled receptor kinase 6       37011_at   down   0.041037942   allograft inflammatory factor 1       40430_at   up   0.041117487   hypothetical protein FLJ35779       40439_at   down   0.041157278   arsA arsenite transporter, ATP-binding, homolog 1 (bacterial)       36745_at   up   0.041195119       39105_at   down   0.041201015   vasodilator-stimulated phosphoprotein       37941_at   up   0.041220219   myosin binding protein C, fast type       1806_at   up   0.041223406   MCF.2 cell line derived transforming sequence       34049_at   down   0.041282808       41718_g_at   up   0.041288593   fatty acid desaturase 1       34738_at   up   0.041289183   serine hydroxymethyltransferase 1 (soluble)       40379_at   up   0.041411241   cytochrome P450, family 2, subfamily E, polypeptide 1       32646_at   up   0.041464958   KIAA0449 protein       720_at   up   0.041465792   heat shock transcription factor 4       33151_s_at   up   0.041485117   disrupter of silencing 10       39970_at   up   0.041555279   nuclear receptor subfamily 0, group B, member 1       375_at   up   0.041589703   glutathione S-transferase theta 1       33697_at   up   0.041601882   purinergic receptor P2X, ligand-gated ion channel, 7       420_at   up   0.041622259   melanocortin 2 receptor (adrenocorticotropic hormone)       40733_f_at   up   0.041645239   msh homeo box homolog 2 ( Drosophila )       763_at   down   0.041702481   glia maturation factor, beta       2005_s_at   up   0.0417241   Janus kinase 3 (a protein tyrosine kinase, leukocyte)       41651_at   down   0.041743121   KIAA1033 protein       35991_at   down   0.041767326   LSM6 homolog, U6 small nuclear RNA associated ( S. cerevisiae )       38814_at   down   0.041813234   ATPase, H+ transporting, lysosomal 13 kDa, V1 subunit G isoform 1       38548_at   up   0.041829912   cytochrome P450, family 2, subfamily C, polypeptide 8       38312_at   up   0.041984212       37955_at   down   0.042020127   transmembrane protein 4       31357_at   up   0.042037339       34192_at   down   0.042048499   KIAA0532 protein       33336_at   up   0.042053513   solute carrier family 4, anion exchanger, member 1 (erythrocyte                   membrane protein band 3, Diego blood group)       632_at   up   0.042123503   glycogen synthase kinase 3 alpha       1168_at   up   0.042146694   protocadherin beta 17 pseudogene       38794_at   down   0.042176671   upstream binding transcription factor, RNA polymerase I       36562_at   up   0.042240759   KIAA0427 gene product       36952_at   up   0.042241044   hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A                   thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha                   subunit       37994_at   down   0.042302692   fragile X mental retardation 1       1750_at   up   0.042309315   phenylalanine-tRNA synthetase-like       1914_at   up   0.042374368   cyclin A1       37330_at   up   0.0424156   aldehyde dehydrogenase 4 family, member A1       36939_at   up   0.042424587   glycoprotein M6A       32573_at   down   0.042442348   splicing factor, arginine/serine-rich 9       33997_at   up   0.042551104       1875_f_at   up   0.042561561   postmeiotic segregation increased 2-like 3       35953_at   up   0.042571185   carboxypeptidase N, polypeptide 1, 50 kD       32258_r_at   down   0.042616045   telomeric repeat binding factor (NIMA-interacting) 1       32493_at   up   0.04264112   thyrotrophic embryonic factor       41557_at   down   0.042735256   KIAA0052 protein       35673_at   up   0.042751453   Rho guanine nucleotide exchange factor (GEF) 5       1255_g_at   up   0.042771637   guanylate cyclase activator 1A (retina)       648_at   up   0.042778333   arginine vasopressin receptor 1B       1574_s_at   up   0.042812441   interleukin 4       1380_at   up   0.042829999   fibroblast growth factor 7 (keratinocyte growth factor)       40701_at   up   0.042832741   ubiquitin specific protease 13 (isopeptidase T-3)       33945_at   down   0.042849117   tumor necrosis factor (ligand) superfamily, member 5 (hyper-IgM                   syndrome)       40731_at   up   0.04287054   chromobox homolog 5 (HP1 alpha homolog,  Drosophila )       33637_g_at   up   0.042880647   cancer/testis antigen 1       1115_at   down   0.042942517   platelet factor 4 (chemokine (C—X—C motif) ligand 4)       37977_at   up   0.042975756   deltex homolog 2 ( Drosophila )       34809_at   down   0.042989623   KIAA0999 protein       38105_at   down   0.04300635   hypothetical protein FLJ11021 similar to splicing factor,                   arginine/serine-rich 4       33522_at   up   0.043053962   agouti signaling protein, nonagouti homolag (mouse)       32717_at   up   0.043086938   neuralized-like ( Drosophila )       1377_at   down   0.043126879   nuclear factor of kappa light polypeptide gene enhancer in B-cells                   1 (p105)       36596_r_at   up   0.043217487   glycine amidinotransferase (L-arginine:glycine amidinotransferase       AFFX-BioDn-3_at   up   0.043247969       1477_s_at   up   0.04330999   cytochrome P450, family 2, subfamily C, polypeptide 18       39842_at   up   0.043318734   cytokine receptor-like factor 1       1903_at   down   0.043361718       40777_at   down   0.04336893   catenin (cadherin-associated protein), beta 1, 88 kDa       34636_at   up   0.043370973   arachidonate 15-lipoxygenase       39645_r_at   up   0.043372248   arrestin 3, retinal (X-arrestin)       41764_at   down   0.043388296   apolipoprotein C-I       36488_at   down   0.043398698   EGF-like-domain, multiple 5       491_at   up   0.04341321   protein tyrosine phosphatase, receptor type, G       37218_at   up   0.043488344   BTG family, member 3       33498_at   up   0.043497555   regenerating islet-derived-like, pancreatic stone protein-like,                   pancreatic thread protein-like (rat)       640_at   up   0.043523098   angiotensin II receptor-like 2       36845_at   down   0.043540169   nuclear matrix protein NXP2       35783_at   down   0.043700506   vesicle-associated membrane protein 3 (cellubrevin)       38529_at   up   0.043708018   acetyl-Coenzyme A carboxylase beta       31947_r_at   up   0.043725153   forkhead box G1A       40689_at   down   0.043739673   sel-1 suppressor of lin-12-like ( C. elegans )       34088_at   up   0.043767248   neurexophilin 4       34884_at   up   0.043790003   carbamoyl-phosphate synthetase 1, mitochondrial       35056_at   up   0.043793206   arylsulfatase F       37348_s_at   down   0.043822957   high mobility group nucleosomal binding domain 3       40132_g_at   down   0.04383039   follistatin-like 1       34422_r_at   up   0.043832201   uncoupling protein 3 (mitochondrial, proton carrier)       36659_at   up   0.043859511   collagen, type IV, alpha 2       35722_at   down   0.04386591   UPF2 regulator of nonsense transcripts homolog (yeast)       34356_at   down   0.043974258   SRB7 suppressor of RNA polymerase B homolog (yeast)       33540_at   up   0.044014718       296_at   down   0.04402855       41147_at   down   0.044084481   hypothetical protein MGC4276 similar to CG8198       40610_at   down   0.044101702   zinc finger RNA binding protein       41208_at   down   0.044106895   S164 protein       31986_at   up   0.044122485       39462_s_at   up   0.044182359   cyclin M2       40958_at   up   0.044246117   KIAA0599 protein       39063_at   up   0.044305104   actin, alpha, cardiac muscle       36754_at   up   0.044401821   adenylate cyclase activating polypeptide 1 (pituitary)       975_at   up   0.04454837   serine/threonine kinase 18       41543_at   up   0.044555245   lymphoid nuclear protein related to AF4       39821_s_at   up   0.04462269   growth arrest and DNA-damage-inducible, beta       38942_r_at   up   0.044661343   AD024 protein       39834_at   up   0.044677883   cholinergic receptor, nicotinic, epsilon polypeptide       41158_at   up   0.044679844   proteolipid protein 1 (Pelizaeus-Merzbacher disease, spastic                   paraplegia 2, uncomplicated)       35954_at   up   0.044713   prodynorphin       38952_s_at   up   0.04475812   collagen, type XIII, alpha 1       1731_at   up   0.044857816   platelet-derived growth factor receptor, alpha polypeptide       40067_at   down   0.044859698   E74-like factor 1 (ets domain transcription factor)       38174_at   up   0.044860824   pleckstrin and Sec7 domain protein       1473_s_at   up   0.044866751   v-myb myeloblastosis viral oncogene homolog (avian)       34475_at   up   0.044903408       39095_at   up   0.044919175   myosin, heavy polypeptide 7, cardiac muscle, beta       34771_at   up   0.044938431   phosphatidic acid phosphatase type 2C       39824_at   up   0.04494232   protein tyrosine phosphatase type IVA, member 3       33583_r_at   up   0.044980903   RNA binding motif, single stranded interacting protein       38567_at   down   0.045086218   CD1D antigen, d polypeptide       33213_g_at   up   0.04509451   ribosome binding protein 1 homolog 180 kDa (dog)       34799_at   up   0.045130417   intraflagellar transport protein IFT20       31708_at   down   0.045135218   ribosomal protein L30       39187_at   up   0.045161232   runt-related transcription factor 2       39175_at   down   0.045229902   phosphofructokina       38340_at   up   0.045251115   huntingtin interacting protein-1-related       38919_at   up   0.045257342   chromosome 6 open reading frame 84       32836_at   up   0.045281983   1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic                   acid acyltransferase, alpha)       AFFX-BioB-M_st   up   0.045314371       110_at   up   0.045320404   chondroitin sulfate proteoglycan 4 (melanoma-associated)       36457_at   down   0.045332883   guanine monphosphate synthetase       1038_s_at   down   0.045424969   interferon gamma receptor 1       32707_at   up   0.045428446   katanin p60 (ATPase-containing) subunit A 1       40772_at   up   0.04548016   hypothetical protein FLJ22269       36995_at   up   0.045488385   alpha-1-microglobulin/bikunin precursor       37439_at   up   0.045504275   solute carrier family 30 (zinc transporter), member 4       32023_at   up   0.045513124       40975_s_at   up   0.04553262   tuftelin interacting protein 11       39684_at   up   0.045568029   membrane protein, palmitoylated 3 (MAGUK p55 subfamily                   member 3)       33534_at   up   0.045610323   endothelial cell-specific molecule 1       39738_at   down   0.045611646   myosin, heavy polypeptide 9, non-muscle       36171_at   down   0.045654778   activated RNA polymerase II transcription cofactor 4       34885_at   up   0.045703542   synaptogyrin 2       32525_r_at   up   0.045882979   junctional adhesion molecule 3       41206_r_at   down   0.045915305   cytochrome c oxidase subunit VIa polypeptide 1       31858_at   down   0.045925116   nuclear transport factor 2       32480_at   up   0.045946721   homeo box C4       37801_at   up   0.045990579   ATPase, H+ transporting, lysosomal V0 subunit a isoform 2       41211_at   up   0.045997988   RNA binding motif protein 12       40326_at   up   0.046028247   cerebellin 1 precursor       35425_at   up   0.046028539   BarH-like homeobox 2       38447_at   up   0.046105867   adrenergic, beta, receptor kinase 1       36687_at   down   0.046108202   cytochrome c oxidase subunit VIIb       1648_at   up   0.046115812   oncostatin M receptor       41386_i_at   up   0.046126282   KIAA0346 protein       34182_at   up   0.046136684   N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1       37084_at   up   0.04615034   lysozyme homolog       37102_at   up   0.046158495   breast cancer metastasis-suppressor 1       38888_at   up   0.046186078   leucine-rich, glioma inactivated 1       36333_at   down   0.046189903   ribosomal protein L7       33404_at   up   0.046205759   adenylyl cyclase-associated protein 2       41321_s_at   up   0.046241974   nucleolar protein family A, member 2 (H/ACA small nucleolar                   RNPs)       1406_at   up   0.046355671   nuclear receptor subfamily 2, group C, member 1       33897_at   up   0.046389018   phosphatidylinositol 4-kinase type II       34280_at   up   0.046453241   gamma-aminobutyric acid (GABA) A receptor, epsilon       1037_at   up   0.046542336   B melanoma antigen       40901_at   down   0.046554909   striatin, calmodulin binding protein 3       38311_at   down   0.046571724   TGFB-induced factor 2 (TALE family homeobox)       37449_i_at   down   0.046577216   GNAS complex locus       506_s_at   up   0.046586309   signal transducer and activator of transcription 5A       38820_at   down   0.046590628   15 kDa selenoprotein       40138_at   up   0.046591745   COP9 subunit 6 (MOV34 homolog, 34 kD)       38075_at   down   0.046592172   synaptophysin-like protein       32705_at   up   0.04659497   cytochrome P450, family 3, subfamily A, polypeptide 7       38328_at   down   0.046624433   solute carrier family 25, member 13 (citrin)       33931_at   down   0.046631191   glutathione peroxidase 4 (phospholipid hydroperoxidase)       1388_g_at   down   0.046638995   vitamin D (1,25-dihydroxyvitamin D3) receptor       36396_at   up   0.046663781       31878_at   down   0.046669447   ATP-binding cassette, sub-family F (GCN20), member 2       35727_at   down   0.046749257   uridine kinase-like 1       31824_at   up   0.046757144   malic enzyme 1, NADP(+)-dependent, cytosolic       34741_at   up   0.046861972   transcription factor Dp-2 (E2F dimerization partner 2)       39189_at   up   0.046938514   potassium voltage-gated channel, Shaw-related subfamily,                   member 4       37195_at   up   0.046947354   cytochrome P450, family 11, subfamily A, polypeptide 1       41778_at   up   0.046964409   solute carrier family 1 (neutral amino acid transporter), member 5       40561_at   up   0.046977023   T-cell leukemia, homeobox 2       31318_at   up   0.047010382       31985_at   up   0.047097209   pleckstrin homology domain interacting protein       31571_at   up   0.047105137   polymerase (RNA) III (DNA directed) (32 kD)       34179_at   up   0.047151817   zinc finger protein 297       39005_s_at   down   0.047173316   zinc finger protein 294       39634_at   up   0.047190272   slit homolog 2 ( Drosophila )       38359_at   up   0.047233322   RAS guanyl releasing protein 2 (calcium and DAG-regulated)       39767_at   down   0.047273537   chaperonin containing TCP1, subunit 8 (theta)       35368_at   down   0.047276393   zinc finger protein 207       40727_at   down   0.047283047   anaphase-promoting complex subunit 10       38593_r_at   up   0.047357278   KIAA0284 protein       2010_at   down   0.047362414   S-phase kinase-associated protein 1A (p19A)       35575_f_at   up   0.047365962   zinc finger protein 253       1910_s_at   up   0.04741841   B-cell CLL/lymphoma 2       184_at   up   0.047445638   angiotensin II receptor-like 1       38461_at   up   0.04746726   nebulin       38997_at   up   0.047512317   solute carrier family 25 (mitochondrial carrier; citrate transporter),                   member 1       38449_at   up   0.047540057   WD repeat domain 23       36511_at   down   0.047649025   SAC1 suppressor of actin mutations 1-like (yeast)       39660_at   up   0.047681544   defensin, beta 1       1134_at   up   0.04771627   activated p21cdc42Hs kinase       350_at   down   0.047748166   zinc finger protein 161       38108_at   up   0.047777085   palmitoyl-protein thioesterase 2       41572_r_at   down   0.047800461   v-rel reticuloendotheliosis viral oncogene homolog (avian)       36430_at   up   0.047801528   adrenomedullin receptor       183_at   up   0.047811102   microtubule-associated protein 2       33424_at   down   0.047825363   ribophorin I       36289_f_at   up   0.047833702   fucosyltransferase 6 (alpha (1,3) fucosyltransferase)       352_at   up   0.047842757   phosphotidylinositol transfer protein       37481_at   down   0.047846427   cell division cycle 40 homolog (yeast)       38671_at   up   0.04786849   plexin D1       36421_at   up   0.04790502       40687_at   up   0.047916691   gap junction protein, alpha 4, 37 kDa (connexin 37)       33903_at   up   0.047941918   death-associated protein kinase 3       40002_r_at   up   0.048072194   chorea acanthocytosis       33309_at   down   0.048101663   comparative gene identification 58       40831_at   down   0.048137628   DKFZP586B0923 protein       35907_at   up   0.048159735   cyclin F       494_at   up   0.048164571   interleukin 13       32112_s_at   down   0.048170984   absent in melanoma 1       34253_at   down   0.048212712   nucleoporin 160 kDa       36998_s_at   down   0.048223756   spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal                   dominant, ataxin 2)       34217_at   up   0.048263151   Kruppel-like factor 7 (ubiquitous)       671_at   down   0.048295042   secreted protein, acidic, cysteine-rich (osteonectin)       36934_at   down   0.048313588   chromosome 20 open reading frame 111       33589_at   up   0.048381236       34811_at   down   0.048384646   ATP synthase, H+ transporting, mitochondrial F0 complex, subun                   c (subunit 9) isoform 3       41420_at   down   0.048387986   insulin-like growth factor binding protein 5       1961_f_at   up   0.048390228   nitric oxide synthase 3 (endothelial cell)       32778_at   down   0.048408   inositol 1,4,5-triphosphate receptor, type 1       1376_at   up   0.048423676   ligase I, DNA, ATP-dependent       31648_at   up   0.048427152   chromosome 6 open reading frame 54       36533_at   up   0.048431505   prostaglandin I2 (prostacyclin) synthase       691_g_at   up   0.048436464   procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-                   hydroxylase), beta polypeptide (protein disulfide isomerase;                   thyroid hormone binding protein p55)       823_at   up   0.048447199   chemokine (C—X3—C motif) ligand 1       39254_at   up   0.048494182   retinoic acid induced 14       31826_at   up   0.04850013   KIAA0674 protein       35247_at   down   0.048510979   small nuclear RNA activating complex, polypeptide 5, 19 kDa       777_at   down   0.048547239   GDP dissociation inhibitor 2       36561_at   down   0.048563389   propionyl Coenzyme A carboxylase, beta polypeptide       32597_at   down   0.048567647   retinoblastoma-like 2 (p130)       39315_at   up   0.048579702   angiopoietin 1       33099_at   up   0.048604195   fucosyltransferase 5 (alpha (1,3) fucosyltransferase)       37383_f_at   up   0.048648959   major histocompatibility complex, class I, C       36479_at   up   0.048655756   growth arrest-specific 8       35804_at   down   0.04866351   ash2 (absent, small, or homeotic)-like ( Drosophila )       39258_at   down   0.048682346   ring finger protein 126       31560_at   up   0.04868959   interleukin 1 receptor-like 2       34694_at   up   0.048706288   SWI/SNF related, matrix associated, actin dependent regulator of                   chromatin, subfamily d, member 2       37398_at   down   0.04874917   platelet/endothelial cell adhesion molecule (CD31 antigen)       33701_at   up   0.048783164   phenylalanine hydroxylase       40338_at   up   0.048799432       38047_at   up   0.048809968   RNA binding protein with multiple splicing       1552_i_at   up   0.048820655   cytochrome P450, family 2, subfamily A, polypeptide 13       32997_at   up   0.04888841   G antigen, family B, 1 (prostate associated)       33506_at   up   0.048920322   inositol polyphosphate-4-phosphatase, type I, 107 kDa       36257_at   up   0.049004519       896_at   up   0.049060786   mucin 2, intestinal/tracheal       37101_at   up   0.049085465   breast cancer metastasis-suppressor 1       37612_at   up   0.049087566   parvalbumin       33636_at   up   0.0490977   cancer/testis antigen 1       31349_at   up   0.049121601   DNA-binding protein amplifying expression of surfactant protein B       39624_at   up   0.049180262   leukotriene B4 receptor       33327_at   up   0.04919815   chromosome 11 open reading frame 9       33952_at   up   0.049220745   zinc finger protein 306       34631_at   up   0.04924553   eyes absent homolog 4 ( Drosophila )       33890_at   up   0.049248261   regulator of G-protein signalling 5       33646_g_at   up   0.049269594   GM2 ganglioside activator protein       39065_s_at   down   0.049283287   tetratricopeptide repeat domain 3       32783_at   up   0.049303682   fibulin 2       35843_at   down   0.049309055   NIMA (never in mitosis gene a)-related kinase 9       41613_at   up   0.04933168   KIAA0329 gene product       33912_at   down   0.049387377   zinc metalloproteinase (STE24 homolog, yeast)       34093_at   up   0.049407315       32772_s_at   up   0.049413791   UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 1       34402_at   down   0.049425825   unr-interacting protein       39372_at   down   0.049477707   fatty acid desaturase 1       1254_at   up   0.04948114   guanylate cyclase activator 1A (retina)       36121_at   up   0.049509564   epsin 2       33011_at   up   0.049521701   neurotensin receptor 2       37732_at   down   0.049539909   RING1 and YY1 binding protein       36863_at   up   0.049676408   hyaluronan-mediated motility receptor (RHAMM)       36010_at   up   0.049689666   mesenchyme homeo box 1       38355_at   down   0.049749088   DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide, Y chromosome       41594_at   down   0.049757578   Janus kinase 1 (a protein tyrosine kinase)       37538_at   up   0.049804213       41864_at   up   0.04983549       447_g_at   down   0.0498497   casein kinase 1, gamma 2       1647_at   down   0.049914966   IQ motif containing GTPase activating protein 2       38666_at   down   0.050017281   pleckstrin homology, Sec7 and coiled-coil domains 1 (cytohesin 1)       37074_at   up   0.05006693   syntrophin, beta 1 (dystrophin-associated protein A1, 59 kDa, basi                   component 1)       38753_at   down   0.050071335   exportin, tRNA (nuclear export receptor for tRNAs)       37460_at   up   0.050130808   T-cell lymphoma invasion and metastasis 1       32924_at   up   0.050139399   matrix metalloproteinase 24 (membrane-inserted)       33939_at   up   0.05014943   potassium voltage-gated channel, shaker-related subfamily,                   member 1 (episodic ataxia with myokymia)       35942_at   up   0.050154516       41775_at   up   0.050197141   isoprenylcysteine carboxyl methyltransferase       35200_at   up   0.050298469   high mobility group AT-hook 2       34889_at   down   0.050400452   ATPase, H+ transporting, lysosomal 70 kDa, V1 subunit A       40927_at   up   0.050411621   solute carrier family 6 (neurotransmitter transporter, creatine),                   member 8       1170_at   up   0.050472551       34647_at   down   0.050512762   DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 5 (RNA helicase,                   68 kDa)       595_at   down   0.050514625   tumor necrosis factor, alpha-induced protein 3       513_at   up   0.050548181   mitogen-activated protein kinase kinase 5       36567_at   up   0.05061091   solute carrier family 17 (sodium-dependent inorganic phosphate                   cotransporter), member 7       35386_at   up   0.050611701   acetylcholinesterase (YT blood group)       34103_at   up   0.050662538       39176_f_at   up   0.050705598   carboxyl ester lipase (bile salt-stimulated lipase)       34078_s_at   up   0.050714993   cytochrome P450, family 2, subfamily C, polypeptide 19       362_at   up   0.050721464   protein kinase C, zeta       31341_at   up   0.05078886   potassium voltage-gated channel, Shaw-related subfamily,                   member 3       140_s_at   down   0.050824342   splicing factor, arginine/serine-rich 10 (transformer 2 homolog,                     Drosophila )       38486_at   up   0.050860569   troponin I, skeletal, slow       40607_at   down   0.050870068   dihydropyrimidinase-like 2       41563_at   up   0.050883454   transient receptor potential cation channel, subfamily M, member 1       38771_at   down   0.050919217   histone deacetylase 1       36514_at   down   0.050919704   cell growth regulatory with ring finger domain       1689_at   up   0.050938547   protocadherin 16 dachsous-like ( Drosophila )       33287_at   up   0.051003471   hypothetical protein HSPC109       334_s_at   up   0.051007767       35956_s_at   up   0.05102897   pregnancy specific beta-1-glycoprotein 7       39704_s_at   down   0.051031896   high mobility group AT-hook 1       885_g_at   up   0.051041395   integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3                   receptor)       35530_f_at   up   0.051160162   immunoglobulin lambda locus       33458_r_at   down   0.051179962   histone 1, H2bc       1330_at   up   0.051206939   mitogen-activated protein kinase kinase kinase 3       35178_at   up   0.051239142   WNT inhibitory factor 1       36556_at   up   0.051298489   KIAA0672 gene product       34124_at   up   0.051343537   mitochondrial translational release factor 1-like       32869_at   up   0.051360804   MRE11 meiotic recombination 11 homolog A ( S. cerevisiae )       38527_at   down   0.051367943   non-POU domain containing, octamer-binding       38568_at   down   0.051403125   tumor protein p53-binding protein       39023_at   down   0.051454387   isocitrate dehydrogenase 1 (NADP+), soluble       41650_at   up   0.051471647   WD40 protein Ciao1       32582_at   up   0.051507501   myosin, heavy polypeptide 11, smooth muscle       33350_s_at   down   0.051519969   JM5 protein       36098_at   down   0.051540433   splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate                   splicing factor)       35499_at   up   0.051549928   hypothetical protein FLJ11336       31584_at   down   0.051651619   tumor protein, translationally-controlled 1       33660_at   down   0.051688017   ribosomal protein L5       36895_at   down   0.051724914   origin recognition complex, subunit 3-like (yeast)       33228_g_at   down   0.051742066   interleukin 10 receptor, beta       31752_at   up   0.051948954   hypothetical protein FLJ23142       418_at   up   0.051966256   antigen identified by monoclonal antibody Ki-67       39401_at   up   0.052038202   ribosomal protein S13       1343_s_at   up   0.052108915   serine (or cysteine) proteinase inhibitor, clade B (ovalbumin),                   member 3       855_at   down   0.052145184   programmed cell death 2       1174_at   up   0.052217952       37152_at   down   0.052254523   peroxisome proliferative activated receptor, delta       37931_at   up   0.052279349   centromere protein B, 80 kDa       41530_at   down   0.052346679   acetyl-Coenzyme A acyltransferase 2 (mitochondrial 3-oxoacyl-                   Coenzyme A thiolase)       1859_s_at   up   0.05236121   Mdm2, transformed 3T3 cell double minute 2, p53 binding protein                   (mouse)       35975_at   down   0.052380431   myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog,                     Drosophila ); translocated to, 3       33101_g_at   up   0.052389477   fetuin B       1974_s_at   up   0.052421103   tumor protein p53 (Li-Fraumeni syndrome)       1280_i_at   up   0.052503614       38600_r_at   up   0.052520183       35426_at   up   0.052533016   SPPL2b       31978_at   up   0.052541422   kinesin family member 25       38746_at   up   0.052620875   integrin, beta 4       41153_f_at   down   0.052679177   catenin (cadherin-associated protein), alpha 1, 102 kDa       35812_at   up   0.052688828   transportin-SR       40788_at   up   0.052750269   adenylate kinase 2       40324_r_at   up   0.052791746   topoisomerase (DNA) III beta       35271_at   down   0.052803954   ARP3 actin-related protein 3 homolog (yeast)       38910_at   up   0.052829015   ATP synthase mitochondrial F1 complex assembly factor 2       38095_i_at   down   0.052863898   major histocompatibility complex, class II, DP beta 1       35267_g_at   down   0.052865754   bladder cancer associated protein       38945_at   up   0.052875372   metal-regulatory transcription factor 1       38522_s_at   down   0.052897744   CD22 antigen       31567_at   up   0.052906998   gamma-aminobutyric acid (GABA) A receptor, gamma 3       37099_at   down   0.052981643   arachidonate 5-lipoxygenase-activating protein       562_g_at   up   0.053109055   follicle stimulating hormone receptor       33906_at   up   0.053130467   Sjogren&#39;s syndrome/scleroderma autoantigen 1       40846_g_at   down   0.053163872   interleukin enhancer binding factor 3, 90 kDa       34312_at   down   0.053202442   nuclear receptor coactivator 2       38644_at   up   0.053219276   paxillin       33834_at   up   0.053224091   chemokine (C—X—C motif) ligand 12 (stromal cell-derived factor 1)       155_s_at   down   0.053379913   ubiquitin-like 1 (sentrin)       31363_at   up   0.053396497   CCR4-NOT transcription complex, subunit 2       32966_at   up   0.053413878   apolipoprotein F       35227_at   up   0.053429325   retinoblastoma binding protein 8       1537_at   up   0.053442744   epidermal growth factor receptor (erythroblastic leukemia viral (v-                   erb-b) oncogene homolog, avian)       32122_at   up   0.053448125   sulfite oxidase       35515_at   up   0.053507235   tektin 2 (testicular)       40387_at   down   0.053544896   endothelial differentiation, lysophosphatidic acid G-protein-couple                   receptor, 2       1718_at   down   0.053617875   actin related protein 2/3 complex, subunit 2, 34 kDa       33341_at   down   0.053655896   guanine nucleotide binding protein (G protein), beta polypeptide 1       40269_at   down   0.053675027   PRP18 pre-mRNA processing factor 18 homolog (yeast)       37000_at   down   0.053751225   DKFZP564B167 protein       1667_s_at   up   0.053766642   cytochrome P450, family 4, subfamily B, polypeptide 1       37993_at   up   0.053772854   ATP synthase, H+ transporting, mitochondrial F1 complex, delta                   subunit       40883_at   up   0.053801821   syntaxin 16       31420_at   up   0.053822167   immunoglobulin lambda variable (IV)/OR22-1       37980_at   down   0.053851354   CBF1 interacting corepressor       1451_s_at   up   0.05389717   osteopath specific factor 2 (fasciclin I-like)       39118_at   down   0.05391293   DnaJ (Hsp40) homolog, subfamily A, member 1       39265_at   up   0.053944254   type 1 tumor necrosis factor receptor shedding aminopeptidase                   regulator       34569_at   up   0.053973736   SRY (sex determining region Y)-box 11       160_g_at   up   0.054005608       35168_f_at   down   0.054037696   collagen, type XVI, alpha 1       40015_at   up   0.054067609   KIAA0303 protein       36219_at   down   0.054111813   similar to  Caenorhabditis elegans  protein C42C1.9       33068_f_at   up   0.054171933   UDP glycosyltransferase 2 family, polypeptide B15       538_at   up   0.054185653   CD34 antigen       39503_s_at   up   0.054254903   dihydropyrimidinase-like 4       38427_at   up   0.054256236   collagen, type XV, alpha 1       33448_at   up   0.05426235   serine protease inhibitor, Kunitz type 1       36870_at   down   0.054274318   KIAA0804 protein       41680_at   up   0.054307826   chromosome 1 open reading frame 34       38463_s_at   down   0.054344711   adenosine monophosphate deaminase (isoform E)       36362_at   up   0.054379239   solute carrier family 12 (sodium/chloride transporters), member 3       32704_at   down   0.054445472   dedicator of cyto-kinesis 2       39168_at   up   0.054468601   Ac-like transposable element       40587_s_at   down   0.054472775   eukaryotic translation elongation factor 1 epsilon 1       37081_at   up   0.054493153   dynein, axonemal, heavy polypeptide 7       33447_at   down   0.05449949   myosin regulatory light chain MRCL3       33205_at   up   0.054582892   suppressor of Ty 3 homolog ( S. cerevisiae )       41462_at   down   0.054609547   sorting nexin 2       41625_at   down   0.054610798   thyroid hormone receptor-associated protein, 240 kDa subunit       32175_at   down   0.054611527   CDC10 cell division cycle 10 homolog ( S. cerevisiae )       36099_at   down   0.054636307   splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate                   splicing factor)       39349_at   up   0.054649873   HMT1 hnRNP methyltransferase-like 1 ( S. cerevisiae )       38367_s_at   up   0.054689416   complement component 4 binding protein, beta       1474_s_at   up   0.054758106   v-myb myeloblastosis viral oncogene homolog (avian)       40429_r_at   up   0.054807695       40502_r_at   up   0.054812914   myosin binding protein C, slow type       34232_at   up   0.054826808   natural killer-tumor recognition sequence       36148_at   up   0.054862015   amyloid beta (A4) precursor-like protein 1       1040_s_at   up   0.054877884   abl-interactor 2       41692_at   down   0.054891324   synaptojanin 1       32569_at   down   0.054893855   platelet-activating factor acetylhydrolase, isoform lb, alpha subunit                   45 kDa       160030_at   up   0.054898491   growth hormone receptor       32452_at   up   0.054953745   cyclin-dependent kinase 3       36639_at   up   0.054982119   adenylosuccinate lyase       40357_at   up   0.054984105   inhibin, beta A (activin A, activin AB alpha polypeptide)       31437_r_at   up   0.05500989   estrogen receptor 2 (ER beta)       38802_at   down   0.055010478   progesterone receptor membrane component 1       41837_at   up   0.055099827   chromosome 14 open reading frame 132       261_s_at   up   0.055127541   apolipoprotein B (including Ag(x) antigen)       38083_at   down   0.0551325   Notch homolog 2 ( Drosophila )       35611_at   up   0.055135445   zinc finger protein 37 homolog (mouse)       41812_s_at   down   0.055143341   nucleoporin 210       37535_at   down   0.055180046   cAMP responsive element binding protein 1       38800_at   up   0.05524435   stathmin-like 2       41663_at   up   0.0552624       36575_at   up   0.055284709   regulator of G-protein signalling 1       39739_at   down   0.055289363   nascent-polypeptide-associated complex alpha polypeptide       38562_g_at   up   0.055320447   down-regulated in metastasis       41052_s_at   up   0.055330253   calcium channel, voltage-dependent, P/Q type, alpha 1A subunit       39548_at   up   0.055386674   neuronal PAS domain protein 2       31929_at   down   0.055389172   regulatory factor X, 3 (influences HLA class II expression)       1946_at   up   0.055451877   Wilms tumor associated protein       32324_at   down   0.055453311   tyrosine 3-monooxygenase/tryptophan 5-monooxygenase                   activation protein, beta polypeptide       38660_at   up   0.055562135   cytochrome c oxidase subunit VIa polypeptide 2       38370_at   down   0.055580846       32702_at   up   0.055632752   trophinin associated protein (tastin)       41184_s_at   down   0.055648432   proteasome (prosome, macropain) subunit, beta type, 8 (large                   multifunctional protease 7)       33542_at   up   0.05569065       34444_at   up   0.055727944   chromosome X open reading frame 1       33043_at   up   0.055762089   eukaryotic translation elongation factor 1 gamma       34461_at   up   0.055819194   synaptonemal complex protein 1       40243_at   up   0.055858811   metallo phosphoesterase       36599_at   down   0.055883675   malic enzyme 2, NAD(+)-dependent, mitochondrial       32026_s_at   down   0.055895289   PDZ domain containing guanine nucleotide exchange factor (GEF 1       33272_at   up   0.055916736   serum amyloid A1       35412_at   up   0.055920677   cytochrome P450, family 4, subfamily A, polypeptide 11       31753_at   up   0.056077168       32537_at   up   0.05609059   lipidosin       36411_s_at   up   0.056166675   ELAV (embryonic lethal, abnormal vision,  Drosophila )-like 2 (Hu                   antigen B)       31844_at   down   0.056320576   homogentisate 1,2-dioxygenase (homogentisate oxidase)       530_at   up   0.056385304   nuclear factor of kappa light polypeptide gene enhancer in B-cells                   inhibitor-like 2       903_at   down   0.056390908   protein phosphatase 2, regulatory subunit B (B56), alpha isoform       39283_at   up   0.056439846   apical protein-like ( Xenopus laevis )       38406_f_at   up   0.05649877   prostaglandin D2 synthase 21 kDa (brain)       39239_at   up   0.056512111   CD8 antigen, beta polypeptide 1 (p37)       32481_at   up   0.056673095       37808_at   up   0.056785668   sorting nexin 7       37775_at   up   0.056808833   septin 6       938_at   up   0.056826365       34921_at   up   0.056875557   KIAA0420 gene product       36472_at   down   0.056888332   N-myc (and STAT) interactor       33154_at   down   0.05689138   proteasome (prosome, macropain) subunit, beta type, 4       41173_at   up   0.05691759       37651_at   down   0.056919669   REST corepressor       39344_at   down   0.056934629   transformer-2 alpha (htra-2 alpha)       1548_s_at   up   0.056952857   interleukin 10       34574_at   up   0.056969408   melanoma antigen, family A, 11       36493_at   down   0.056992416   lymphocyte-specific protein 1       41243_at   down   0.057169482   solute carrier family 35, member E2       34446_at   down   0.057273151   KIAA0471 gene product       37595_at   up   0.057288566       40317_at   up   0.057307104   amiloride-sensitive cation channel 1, neuronal (degenerin)       1948_f_at   up   0.057328317   nitric oxide synthase 2A (inducible, hepatocytes)       39973_at   up   0.057344468   leprecan-like 2 protein       40785_g_at   down   0.057345337   protein phosphatase 2, regulatory subunit B (B56), gamma                   isoform       32076_at   up   0.057364647   Down syndrome critical region gene 1-like 1       35514_at   up   0.057373421   Rho family guanine-nucleotide exchange factor       41152_f_at   down   0.057442439   ribosomal protein L36a       38395_at   down   0.057443145   NADH dehydrogenase (ubiquinone) Fe—S protein 1, 75 kDa                   (NADH-coenzyme Q reductase)       160042_s_at   up   0.057472079   homeo box B6       388_at   up   0.057530222   phosphoinositide-3-kinase, regulatory subunit, polypeptide 2 (p85                   beta)       41214_at   down   0.057534645   ribosomal protein S4, Y-linked       35969_at   up   0.057696203   M-phase phosphoprotein 9       38023_at   up   0.057706011   phosphotidylinositol transfer protein       39306_at   up   0.057708653   protease, serine, 16 (thymus)       33246_at   up   0.057726548   mitogen-activated protein kinase 13       32809_at   down   0.057746743       37862_at   up   0.057768456   dihydrolipoamide branched chain transacylase (E2 component of                   branched chain keto acid dehydrogenase complex; maple syrup                   urine disease)       1886_at   up   0.057823252   wingless-type MMTV integration site family, member 7A       36519_at   down   0.057885294   excision repair cross-complementing rodent repair deficiency,                   complementation group 1 (includes overlapping antisense                   sequence)       36465_at   up   0.058006837   interferon regulatory factor 5       1236_s_at   up   0.058010665   neurofibromin 1 (neurofibromatosis, von Recklinghausen disease,                   Watson disease)       38299_at   up   0.058034422   interleukin 6 (interferon, beta 2)       35928_at   up   0.058057431   thyroid peroxidase       32029_at   up   0.058077367   3-phosphoinositide dependent protein kinase-1       36104_at   down   0.058084978   ubiquinol-cytochrome c reductase hinge protein       37893_at   down   0.05809969   protein tyrosine phosphatase, non-receptor type 2       713_at   up   0.05811789       32918_at   up   0.058151217       37917_at   down   0.05818336   hypothetical protein FLJ20323       1788_s_at   up   0.058232158   dual specificity phosphatase 4       31769_at   up   0.058233033   wingless-type MMTV integration site family, member 8B       39219_at   down   0.058252593   CCAAT/enhancer binding protein (C/EBP), gamma       416_s_at   up   0.058290651   homeo box C5       33457_at   down   0.058377788   retinoblastoma-associated protein 140       37718_at   down   0.058387995   SNF-1 related kinase       34053_at   up   0.058414295   zona pellucida binding protein       38245_i_at   up   0.058439157   mitogen-activated protein kinase kinase kinase kinase 5       37943_at   down   0.05843963   zinc finger, FYVE domain containing 26       40401_at   up   0.058454018   docking protein 5       39048_at   up   0.0585224   Notch homolog 4 ( Drosophila )       41023_at   up   0.058574201   complement component 8, alpha polypeptide       37824_at   up   0.058584019   KIAA1074 protein       39819_at   up   0.058650541   RNA polymerase I transcription factor RRN3       41231_f_at   down   0.058672904   high-mobility group nucleosomal binding domain 2       682_at   up   0.058711408   interferon, alpha 8       38931_at   down   0.058759428   zinc finger protein, X-linked       40509_at   down   0.058761269   electron-transfer-flavoprotein, alpha polypeptide (glutaric aciduria                   II)       32306_g_at   up   0.058783564   collagen, type I, alpha 2       38223_at   down   0.058796236   TBC1 domain family, member 8 (with GRAM domain)       37920_at   up   0.058825806   paired-like homeodomain transcription factor 1       41821_at   down   0.05885646   cell division cycle 2-like 5 (cholinesterase-related cell division                   controller)       40575_at   up   0.058887769   discs, large ( Drosophila ) homolog 5       33714_at   up   0.058937876   high-mobility group box 3       36778_at   down   0.059000095   ocular albinism 1 (Nettleship-Falls)       369_s_at   up   0.059042852   ubiquitin-conjugating enzyme E2H (UBC8 homolog, yeast)       34612_at   up   0.05904774   calbindin 3, (vitamin D-dependent calcium binding protein)       38364_at   down   0.059052258   B lymphocyte gene 1       40952_at   up   0.059083867   BTG3 associated nuclear protein       1008_f_at   up   0.059087627   protein kinase, interferon-inducible double stranded RNA                   dependent       38930_at   up   0.059243009       37568_at   up   0.059295057       40011_s_at   up   0.059317671   fragile X mental retardation 2       34482_at   down   0.059336699   hypothetical protein MGC4701       38620_at   up   0.059347346   golgi SNAP receptor complex member 2       32641_at   down   0.059370035   androgen-induced proliferation inhibitor       41848_f_at   up   0.059393969   interleukin 24       1446_at   down   0.059425354   proteasome (prosome, macropain) subunit, alpha type, 2       1611_s_at   up   0.059473457   interferon, gamma       34519_at   up   0.05950626   natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic                   peptide receptor C)       34792_at   down   0.059523377   S-adenosylhomocysteine hydrolase-like 1       1787_at   down   0.05953562   cyclin-dependent kinase inhibitor 1C (p57, Kip2)       36975_at   down   0.059558803   hypothetical protein MGC8721       34337_s_at   down   0.05957962   likely ortholog of mouse metal response element binding                   transcription factor 2       39491_s_at   up   0.059588745       37623_at   up   0.059601491   nuclear receptor subfamily 4, group A, member 2       37483_at   down   0.059686507   histone deacetylase 9       937_at   down   0.059741003       32168_s_at   down   0.059758424   Down syndrome critical region gene 1       37524_at   down   0.059785317   serine/threonine kinase 17b (apoptosis-inducing)       31776_at   up   0.059797735       37590_g_at   up   0.059839604       1113_at   up   0.060099594   bone morphogenetic protein 2       34595_at   up   0.060161002   myosin IA       40608_at   down   0.060169789   ribosomal protein S13       36935_at   down   0.060188988   RAS p21 protein activator (GTPase activating protein) 1       32246_g_at   down   0.060205029   chromosome 14 open reading frame 92       34891_at   down   0.060240172   dynein, cytoplasmic, light polypeptide 1       40337_at   up   0.060277334   fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase,                   Bombay phenotype included)       35326_at   up   0.060313969   Yip1 interacting factor homolog ( S. cerevisiae )       38983_at   down   0.060318989   NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6,                   14 kDa       38783_at   up   0.060335185   mucin 1, transmembrane       36597_at   down   0.060379177   nucleolar and coiled-body phosphoprotein 1       1445_at   up   0.060466022   chemokine (C—C motif) receptor-like 2       40212_at   up   0.06048741   kinase suppressor of ras       1057_at   up   0.060533082   cellular retinoic acid binding protein 2       35992_at   up   0.060585199   musculin (activated B-cell factor-1)       40084_at   down   0.060604175   transcription factor CP2       38685_at   down   0.060642908   syntaxin 12       35089_at   up   0.060731492   neuregulin 2       38672_at   up   0.060809774   protein phosphatase 1, regulatory subunit 10       38454_g_at   down   0.060868973   intercellular adhesion molecule 2       34208_at   up   0.060876759   solute carrier family 12, (potassium-chloride transporter) member 5       39278_at   up   0.060889133   transglutaminase 4 (prostate)       37581_at   down   0.060941394   protein phosphatase 6, catalytic subunit       38442_at   up   0.060971291   microfibrillar-associated protein 2       37634_at   up   0.060996525   progestagen-associated endometrial protein (placental protein 14                   pregnancy-associated endometrial alpha-2-globulin, alpha uterine                   protein)       729_i_at   up   0.061028761       33402_at   up   0.061073887   KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention                   receptor 3       41824_at   down   0.061082771   CGI-48 protein       35377_at   up   0.061238393   DKFZP434M154 protein       39205_at   up   0.061272223   hypothetical protein PP1665       584_s_at   down   0.061289672   X-ray repair complementing defective repair in Chinese hamster                   cells 5 (double-strand-break rejoining; Ku autoantigen, 80 kDa)       38261_at   down   0.061331903   ATP-binding cassette, sub-family C (CFTR/MRP), member 3       40937_at   up   0.061382943   zinc finger protein 291       33376_at   up   0.061386605   N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1       39571_at   up   0.0614091   hypothetical protein DKFZp434G2311       36670_at   up   0.061452772   autoantigen       31675_s_at   down   0.06149695   phosphatase and tensin homolog (mutated in multiple advanced                   cancers 1), pseudogene 1       34730_g_at   up   0.061538175   trophinin       41556_s_at   up   0.061577406   heparan sulfate (glucosamine) 3-O-sulfotransferase 1       35737_at   up   0.061613514   high mobility group nucleosomal binding domain 4       36064_at   up   0.061678211   potassium voltage-gated channel, KQT-like subfamily, member 2       34829_at   up   0.061682903   dyskeratosis congenita 1, dyskerin       1592_at   up   0.061762496   topoisomerase (DNA) II alpha 170 kDa       34657_at   down   0.06176476   A kinase (PRKA) anchor protein 11       33254_at   down   0.061846647   ecotropic viral integration site 5       1367_f_at   down   0.061855363   ubiquitin C       38060_at   down   0.061883861   NADH dehydrogenase (ubiquinone) Fe—S protein 5, 15 kDa                   (NADH-coenzyme Q reductase)       33797_at   up   0.06191586   M-phase phosphoprotein 10 (U3 small nucleolar                   ribonucleoprotein)       35294_at   down   0.061934664   Sjogren syndrome antigen A2 (60 kDa, ribonucleoprotein                   autoantigen SS-A/Ro)       39437_at   up   0.061948929   zinc finger protein 289, ID1 regulated       34723_at   down   0.061958734   COX11 homolog, cytochrome c oxidase assembly protein (yeast)       40800_at   up   0.061977237   HN1 like       40300_g_at   up   0.062012415   G-protein coupled receptor       2013_at   up   0.062019318   transcription factor Dp-2 (E2F dimerization partner 2)       398_at   up   0.062027909   DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 18 (Myc-                   regulated)       35700_at   up   0.062054825   chromodomain helicase DNA binding protein 2       37176_at   up   0.0620627   hyaluronoglucosaminidase 1       35906_at   up   0.062070421   solute carrier family 5 (sodium/glucose cotransporter), member 1       38306_at   down   0.062100311   brefeldin A-inhibited guanine nucleotide-exchange protein 1       33943_at   down   0.062127606   ferritin, heavy polypeptide 1       31652_at   up   0.062177255   KIAA1000 protein       39115_at   down   0.06219621   cysteine-rich with EGF-like domains 1       1897_at   up   0.062201284   transforming growth factor, beta receptor III (betaglycan, 300 kDa)       288_s_at   down   0.062457541   lamin B receptor       904_s_at   up   0.06249421   topoisomerase (DNA) II alpha 170 kDa       34544_at   down   0.06257331   zinc finger protein 267       38622_at   up   0.062579122   hypothetical protein BC004409       32099_at   down   0.062599116   scaffold attachment factor B2       33485_at   down   0.062675228   ribosomal protein L4       38778_at   down   0.062677106   KIAA1046 protein       966_at   up   0.0627393   RAD54-like ( S. cerevisiae )       34111_s_at   up   0.062792399       35272_at   down   0.062795602   guanine nucleotide binding protein (G protein), gamma 5       32807_at   down   0.062914078   DKFZP566C134 protein       37913_at   up   0.062920328   dihydrofolate reductase       36226_r_at   up   0.062926066   splicing factor proline/glutamine rich (polypyirmidine tract binding                   protein associated)       39885_at   down   0.062939041   putative dimethyladenosine transferase       34571_at   up   0.063007099   guanine nucleotide binding protein (G protein), alpha transducing                   activity polypeptide 2       39602_at   up   0.063009221   myosin VIIA and Rab interacting protein       34594_at   down   0.063034238   related to the N terminus of tre       40809_at   up   0.063035272   syntrophin, beta 2 (dystrophin-associated protein A1, 59 kDa, basi                   component 2)       40707_at   up   0.06310375   M-phase phosphoprotein 9       33684_at   up   0.0631076   wingless-type MMTV integration site family, member 2B       31973_at   up   0.063114368   calcium channel, voltage-dependent, alpha 1G subunit       32382_at   up   0.063143488   uroplakin 1B       102_at   up   0.0632572   homeodomain interacting protein kinase 3       38818_at   down   0.063335303   serine palmitoyltransferase, long chain base subunit 1       32549_at   up   0.063359153   pregnancy-associated plasma protein A       32780_at   up   0.063441097   bullous pemphigoid antigen 1, 230/240 kDa       37586_at   up   0.063463781   zinc finger protein 142 (clone pHZ-49)       31728_at   up   0.063480732   major histocompatibility complex, class II, DO alpha       33324_s_at   up   0.063481517   cell division cycle 2, G1 to S and G2 to M       33722_at   down   0.063552526   attractin       31618_at   up   0.063629282       37231_at   up   0.063647129   discs, large homolog 7 ( Drosophila )       33295_at   up   0.063653906   Duffy blood group       38344_at   down   0.0636827   Alstrom syndrome 1       630_at   up   0.063683304   dCMP deaminase       39828_at   up   0.063688282   ADP-ribosylation factor-like 7       36932_at   down   0.063720811   general transcription factor IIIC, polypeptide 2, beta 110 kDa       1213_at   down   0.063729631   SFRS protein kinase 2       36757_at   down   0.063735666   histone 1, H3h       41856_at   up   0.063822614       40717_at   up   0.063953051   cathepsin L2       37142_at   up   0.064046062   GDNF family receptor alpha 1       34772_at   up   0.064054956   coronin, actin binding protein, 2B       36060_at   down   0.064069461   signal recognition particle 54 kDa       1291_s_at   up   0.064069798   fibroblast growth factor receptor 4       40029_at   up   0.064078515   EGF-like-domain, multiple 3       37072_at   up   0.064097818   cyclic nucleotide gated channel beta 1       38860_at   up   0.064166427   phosphodiesterase 4C, cAMP-specific (phosphodiesterase E1                   dunce homolog,  Drosophila )       1490_at   up   0.064176408   v-myc myelocytomatosis viral oncogene homolog 1, lung                   carcinoma derived (avian)       38679_g_at   down   0.064193026   small nuclear ribonucleoprotein polypeptide E       31946_s_at   up   0.064273083   forkhead box G1A       38266_at   down   0.064299188   retinoblastoma binding protein 6       33334_at   down   0.064353716   acylphosphatase 1, erythrocyte (common) type       1737_s_at   up   0.064389565   insulin-like growth factor binding protein 4       1781_at   up   0.064434279   ELK1, member of ETS oncogene family       39396_at   down   0.064438229   lysophospholipase I       34063_at   up   0.064446601   RecQ protein-like 5       37230_at   down   0.064472303   KIAA0469 gene product       32265_at   up   0.064485263   nuclear receptor subfamily 4, group A, member 1       40832_s_at   down   0.064506377   lamina-associated polypeptide 1B       35356_at   down   0.064514009   hypothetical protein MGC9651       40539_at   up   0.064543391   myosin IXB       40984_at   up   0.064566113   gamma tubulin ring complex protein (76p gene)       41376_i_at   up   0.064571434   UDP glycosyltransferase 2 family, polypeptide B7       41576_at   up   0.064620473       273_g_at   up   0.064629736   gastrin-releasing peptide       37022_at   up   0.064629783   proline arginine-rich end leucine-rich repeat protein       722_at   up   0.06464731   RCD1 required for cell differentiation1 homolog ( S. pombe )       34077_at   up   0.064651773   chemokine (C—X—C motif) receptor 3       37341_at   up   0.064654132   glutamate dehydrogenase 1       39481_at   up   0.06467974   long-chain fatty-acyl elongase       36436_at   up   0.064760378   leukocyte cell-derived chemotaxin 2       35716_at   up   0.064783583   sulfotransferase family, cytosolic, 1C, member 1       133_at   down   0.064821382   cathepsin C       36312_at   down   0.064882797   serine (or cysteine) proteinase inhibitor, clade B (ovalbumin),                   member 8       41000_at   down   0.064912113   checkpoint suppressor 1       31677_at   up   0.064958769       1528_at   up   0.06500764   hypothetical gene CG030       36864_at   up   0.065008406   peroxisomal biogenesis factor 3       36325_at   up   0.065037727   crystallin, beta A1       33413_at   down   0.065039089   protein tyrosine phosphatase type IVA, member 1       40336_at   up   0.0651239   ferredoxin reductase       41597_s_at   down   0.065192685   SEC22 vesicle trafficking protein-like 1 ( S. cerevisiae )       39536_at   up   0.065201347   homeo box (H6 family) 1       1073_at   down   0.065224227   transcription elongation factor A (SII), 1       39594_f_at   up   0.065236518   metallothionein 1H       32974_at   up   0.065273556   homolog of Yeast RRP4 (ribosomal RNA processing 4), 3′-5′-                   exoribonuclease       37126_at   up   0.065330653   Sjogren syndrome antigen A1 (52 kDa, ribonucleoprotein                   autoantigen SS-A/Ro)       34693_at   down   0.065343616   sialyltransferase       37925_r_at   up   0.065370621   apolipoprotein M       1190_at   up   0.065390496   protein tyrosine phosphatase, receptor type, O       39243_s_at   down   0.065560845   PC4 and SFRS1 interacting protein 2       40333_at   up   0.065610099   bone morphogenetic protein 4       40428_i_at   up   0.065620187       35703_at   down   0.065621274   platelet-derived growth factor alpha polypeptide       33754_at   up   0.065631647   thyroid transcription factor 1       36620_at   down   0.065767238   superoxide dismutase 1, soluble (amyotrophic lateral sclerosis 1                   (adult))       40710_at   up   0.065846675   calmegin       38629_at   up   0.065898386   microtubule-associated protein tau       41395_at   up   0.06595199   carbohydrate (keratan sulfate Gal-6) sulfotransferase 1       32489_at   up   0.065955036   glutamate receptor, ionotropic, N-methyl D-aspartate 2B       35022_at   up   0.065980914   SRY (sex determining region Y)-box 5       33861_at   down   0.066186823   CCR4-NOT transcription complex, subunit 2       39394_at   up   0.066198374       32986_s_at   up   0.066223752   MAD, mothers against decapentaplegic homolog 9 ( Drosophila )       1707_g_at   up   0.066240761   v-raf murine sarcoma 3611 viral oncogene homolog 1       35078_at   up   0.066266338   intercellular adhesion molecule 4, Landsteiner-Wiener blood group       32846_s_at   down   0.066279462   kinectin 1 (kinesin receptor)       39615_at   up   0.066293934   KIAA1026 protein       39552_at   down   0.06636328   phosphatase and tensin homolog (mutated in multiple advanced                   cancers 1)       41297_at   up   0.066367138   mannosidase, alpha, class 1A, member 2       36290_s_at   up   0.0663784   fucosyltransferase 6 (alpha (1,3) fucosyltransferase)       33367_s_at   down   0.066406849   ornithine decarboxylase antizyme inhibitor       40536_f_at   up   0.066482666   translation initiation factor IF2       32148_at   up   0.066539346   FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1                   (chondrocyte-derived)       1542_at   up   0.066618173   epidermal growth factor (beta-urogastrone)       31419_r_at   up   0.066633328       39096_at   down   0.066635074   SON DNA binding protein       34762_at   up   0.066729339   ring finger protein (C3HC4 type) 8       36672_at   down   0.066753245   prolylcarboxypeptidase (angiotensinase C)       39475_at   up   0.066768992   chromosome 4 open reading frame 9       947_at   up   0.066788523   MCM7 minichromosome maintenance deficient 7 ( S. cerevisiae )       894_g_at   up   0.06685321   ubiquitin carrier protein       34654_at   down   0.066869319   myotubularin related protein 1       36449_s_at   up   0.066888403   peptide YY       40125_at   down   0.066905911   calnexin       39629_at   up   0.066929858   phospholipase A2, group V       40444_s_at   up   0.066945781   catenin (cadherin-associated protein), delta 1       581_at   up   0.066955198   laminin, beta 1       38715_at   up   0.066966094   glycophorin B (includes Ss blood group)       32835_at   down   0.066974462   sudD suppressor of bimD6 homolog ( A. nidulans )       39510_r_at   down   0.067021841   programmed cell death 4 (neoplastic transformation inhibitor)       41535_at   down   0.06707185   CDK2-associated protein 1       32667_at   up   0.067095946   collagen, type IV, alpha 5 (Alport syndrome)       31971_at   up   0.067178117   putative GR6 protein       789_at   up   0.067241382   early growth response 1       39636_at   up   0.067253181       31765_at   up   0.067273333   KIAA0694 gene product       35776_at   up   0.067316705   intersectin 1 (SH3 domain protein)       39125_at   up   0.067337952   transient receptor potential cation channel, subfamily C, member 1       34384_at   down   0.067348878   ATP-binding cassette, sub-family C (CFTR/MRP), member 1       1540_f_at   up   0.067365851   interferon, alpha 5       961_at   up   0.067375409   neurofibromin 1 (neurofibromatosis, von Recklinghausen disease,                   Watson disease)       35069_at   up   0.067384697   hypothetical protein similar to preferentially expressed antigen of                   melanoma       32754_at   up   0.067393559   tropomyosin 3       33872_at   up   0.067430249   latrophilin 2       701_s_at   up   0.067454963       32380_at   up   0.067457336   plakophilin 1 (ectodermal dysplasia/skin fragility syndrome)       34749_at   down   0.06748559   solute carrier family 31 (copper transporters), member 2       40980_at   up   0.067495072   helicase with SNF2 domain 1       39327_at   up   0.067577451   Melanoma associated gene       31663_at   up   0.06777859   myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog,                     Drosophila ); translocated to, 4       39148_s_at   up   0.067828539   alpha thalassemia/mental retardation syndrome X-linked (RAD54                   homolog,  S. cerevisiae )       36616_at   down   0.06785433   DAZ associated protein 2       37530_s_at   up   0.067868284   reelin       41091_at   down   0.067977726   fetal Alzheimer antigen       35064_at   up   0.067980534   tripartite motif-containing 31       40153_at   down   0.067983399   transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)       34623_at   up   0.06798768   defensin, alpha 5, Paneth cell-specific       39036_g_at   down   0.068092911   progestin induced protein       33886_at   down   0.068114085   spectrin SH3 domain binding protein 1       40815_g_at   down   0.068233922   iduronate 2-sulfatase (Hunter syndrome)       1000_at   up   0.068270711   mitogen-activated protein kinase 3       41296_s_at   down   0.068276144   START domain containing 7       38648_at   down   0.06827716   zinc finger protein 384       1994_at   up   0.068310712   activating transcription factor 2       35781_g_at   up   0.068345587   KIAA0657 protein       37235_g_at   up   0.068372273   kininogen       32639_at   up   0.068383912   nucleoporin-like protein 1       41470_at   up   0.068392895   prominin 1       723_s_at   down   0.068462859       39180_at   down   0.068510684   fusion, derived from t(12; 16) malignant liposarcoma       33905_at   down   0.068659685   methyl-CpG binding domain protein 2       38459_g_at   up   0.068816314   cytochrome b-5       36673_at   down   0.068888528   mannose phosphate isomerase       160036_at   up   0.068911333   estrogen-related receptor beta       31660_at   up   0.068977387   DKFZP434A062 protein       38200_at   up   0.069062386   faciogenital dysplasia (Aarskog-Scott syndrome)       33651_at   up   0.069111018   aquaporin 8       842_at   up   0.069200967   protein kinase C binding protein 1       208_at   up   0.069215423   catenin (cadherin-associated protein), alpha 2       37140_s_at   up   0.069281532   ectodermal dysplasia 1, anhidrotic       32418_at   up   0.069291623   phosphodiesterase 1C, calmodulin-dependent 70 kDa       36214_at   down   0.069400426   Kruppel-like factor 4 (gut)       36685_at   down   0.069578272   adenosylmethionine decarboxylase 1       36311_at   up   0.0696169   phosphodiesterase 1A, calmodulin-dependent       35675_at   up   0.06965234   vinexin beta (SH3-containing adaptor molecule-1)       40162_s_at   up   0.069667733   cartilage oligomeric matrix protein (pseudoachondroplasia,                   epiphyseal dysplasia 1, multiple)       38102_at   down   0.069691466   hypothetical protein FLJ34588       193_at   down   0.069842253   TAF9 RNA polymerase II, TATA box binding protein (TBP)-                   associated factor, 32 kDa       32039_at   down   0.069879541   adaptor-related protein complex 3, beta 1 subunit       35604_at   up   0.069916727   endonuclease G-like 1       39346_at   down   0.069917202   KH domain containing, RNA binding, signal transduction                   associated 1       35844_at   up   0.070023077   syndecan 4 (amphiglycan, ryudocan)       711_at   up   0.070029379       39378_at   down   0.070031282   beclin 1 (coiled-coil, myosin-like BCL2 interacting protein)       2017_s_at   up   0.070139758   cyclin D1 (PRAD1: parathyroid adenomatosis 1)       41361_at   up   0.070337448   CCR4-NOT transcription complex, subunit 8       36387_at   up   0.070387113       40569_at   up   0.070393476   zinc finger protein 42 (myeloid-specific retinoic acid-responsive)       40489_at   up   0.070419101   dentatorubral-pallidoluysian atrophy (atrophin-1)       37650_at   down   0.070599809   makorin, ring finger protein, 1       1798_at   down   0.07062824   LIV-1 protein, estrogen regulated       35881_at   up   0.070726932       40545_at   down   0.070878906   proline synthetase co-transcribed homolog (bacterial)       41839_at   up   0.0708905   growth arrest-specific 1       32282_at   up   0.070924055       39210_at   up   0.070930588   fucosyltransferase 4 (alpha (1,3) fucosyltransferase, myeloid-                   specific)       31558_at   up   0.070984093   Hr44 antigen       34383_at   down   0.070998576   ubiquitin specific protease 1       33179_at   up   0.071011949   protein phosphatase 1, regulatory (inhibitor) subunit 2       36598_s_at   up   0.071022431   inositol polyphosphate phosphatase-like 1       390_at   up   0.071049442   chemokine (C—C motif) receptor 4       33526_at   up   0.071061356   neuropeptide Y receptor Y2       1748_s_at   up   0.071122402   Kruppel-like factor 1 (erythroid)       40835_at   up   0.071138085   metastasis-associated 1-like 1       36669_at   up   0.071169146   FBJ murine osteosarcoma viral oncogene homolog B       33162_at   down   0.071262469   insulin receptor       35039_at   up   0.071324095   KIAA0276 protein       33390_at   up   0.071340473   serine/threonine kinase 17b (apoptosis-inducing)       33044_f_at   up   0.071406367   empty spiracles homolog 1 ( Drosophila )       33248_at   up   0.071526167       37409_at   down   0.07160345   SFRS protein kinase 2       31783_at   down   0.071657185   renin binding protein       41080_at   up   0.071729743   H2A histone family, member B       519_g_at   up   0.071740889   nuclear receptor subfamily 1, group H, member 2       38079_at   up   0.07176621   guanine nucleotide binding protein (G protein), gamma 12       41723_s_at   down   0.071880267   major histocompatibility complex, class II, DR beta 1       37560_at   up   0.0719212   FLJ00133 protein       32867_at   up   0.071922807   choroideremia (Rab escort protein 1)       41803_g_at   up   0.072091533   hypothetical protein FLJ22531       419_at   up   0.072110323   antigen identified by monoclonal antibody Ki-67       39146_at   up   0.07212862   alpha thalassemia/mental retardation syndrome X-linked (RAD54                   homolog,  S. cerevisiae )       41175_at   down   0.072189347   core-binding factor, beta subunit       34491_at   up   0.072260618   2′-5′-oligoadenylate synthetase-like       36683_at   up   0.072283268   matrix Gla protein       37598_at   down   0.072298575   Ras association (RaIGDS/AF-6) domain family 2       37403_at   down   0.072370544   annexin A1       35862_at   up   0.072384347   solute carrier family 15 (H+/peptide transporter), member 2       34242_at   up   0.072461287   chromosome 20 open reading frame 194       331_at   up   0.072463612       41638_at   down   0.072496969   KIAA0073 protein       215_g_at   up   0.072524414   msh homeo box homolog 1 ( Drosophila )       31642_at   up   0.072608877       36322_at   up   0.072612703   fucosyltransferase 7 (alpha (1, 3) fucosyltransferase)       812_at   down   0.07262422   protein phosphatase 1, regulatory (inhibitor) subunit 2       41345_at   up   0.072637402   purine-rich element binding protein A       34940_at   down   0.072766213       35909_at   up   0.072779379   pleckstrin homology-like domain, family A, member 1       38856_at   up   0.072867435   KIAA1233 protein       37911_at   up   0.072887305   syntaxin 4A (placental)       36373_at   up   0.072953876   zinc finger, X-linked, duplicated A       37751_at   down   0.07295976   KIAA0255 gene product       39733_at   down   0.073064777   homocysteine-inducible, endoplasmic reticulum stress-inducible,                   ubiquitin-like domain member 1       33337_at   down   0.073072611   degenerative spermatocyte homolog, lipid desaturase ( Drosophila )       35718_at   down   0.07317749   SP110 nuclear body protein       32253_at   down   0.073249284   arginine-glutamic acid dipeptide (RE) repeats       37229_at   down   0.07336482   ataxia telangiectasia and Rad3 related       34912_at   up   0.073371211   death-associated protein kinase 2       41008_at   up   0.073394717   KIAA0888 protein       41286_at   up   0.073511778   tumor-associated calcium signal transducer 2       1476_s_at   up   0.073525062   v-myb myeloblastosis viral oncogene homolog (avian)       657_at   up   0.073549188   protocadherin gamma subfamily C, 3       40698_at   down   0.073559018   C-type (calcium dependent, carbohydrate-recognition domain)                   lectin, superfamily member 2 (activation-Induced)       633_s_at   up   0.073596989   transcription factor Dp-2 (E2F dimerization partner 2)       36006_at   up   0.073614666   SRY (sex determining region Y)-box 12       1930_at   down   0.073728457   ATP-binding cassette, sub-family C (CFTR/MRP), member 3       1123_at   up   0.073740648   growth hormone releasing hormone receptor       33146_at   down   0.073857687   myeloid cell leukemia sequence 1 (BCL2-related)       38575_at   down   0.073876745   mucosa associated lymphoid tissue lymphoma translocation gene 1       36506_at   down   0.073893875   A kinase (PRKA) anchor protein (yotiao) 9       32337_at   down   0.073926169   ribosomal protein L21       37385_at   down   0.073942562   peptidyl-prolyl isomerase G (cyclophilin G)       1585_at   up   0.073949466   v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian       33811_at   down   0.073960943   cell cycle progression 8 protein       37306_at   down   0.073995502   cytoplasmic FMR1 interacting protein 1       35761_at   down   0.07401577   aminoadipate-semialdehyde dehydrogenase-phosphopantetheiny                   transferase       39776_at   up   0.074189511   unc-51-like kinase 2 (C. elegans)       41060_at   up   0.07422555   cyclin E1       37676_at   down   0.07427798   phosphodiesterase 8A       31839_at   down   0.074281268   splicing factor 4       34998_at   down   0.074281619   protein arginine N-methyltransferase 3(hnRNP methyltransferase                     S. cerevisiae )-like 3       2018_at   up   0.074304439   gap junction protein alpha 1, 43 kDa (connexin 43)       41004_at   down   0.074346366   topoisomerase (DNA) III alpha       36571_at   down   0.074361104   topoisomerase (DNA) II beta 180 kDa       33249_at   up   0.074378692   nuclear receptor subfamily 3, group C, member 2       34953_i_at   up   0.074406032   phosphodiesterase 5A, cGMP-specific       1708_at   up   0.074445148   mitogen-activated protein kinase 10       32674_at   down   0.074454592   NP220 nuclear protein       1204_at   up   0.07450712   diacylglycerol kinase, gamma 90 kDa       AFFX-BioC-3_st   up   0.074577771       39353_at   down   0.074613199   heat shock 10 kDa protein 1 (chaperonin 10)       31863_at   down   0.074748576   KIAA0179 protein       38838_at   up   0.074755593   polymyositis/scleroderma autoantigen 1, 75 kDa       36035_at   up   0.074835381   GPAA1P anchor attachment protein 1 homolog (yeast)       40422_at   down   0.074893541   insulin-like growth factor binding protein 2, 36 kDa       34987_s_at   down   0.07495392   heterogeneous nuclear ribonucleoprotein A1       36124_at   up   0.074965842   mercaptopyruvate sulfurtransferase       35657_at   up   0.074965943   TAR (HIV) RNA binding protein 2       36849_at   up   0.074984491   PTPL1-associated RhoGAP 1       32182_at   down   0.074998717   serine/threonine kinase 38 like       32758_g_at   down   0.075062841   RAE1 RNA export 1 homolog ( S. pombe )       461_at   down   0.075106762   N-acylsphingosine amidohydrolase (acid ceramidase) 1       37175_at   up   0.075116156   serine (or cysteine) proteinase inhibitor, clade C (antithrombin),                   member 1       34268_at   down   0.075146357   regulator of G-protein signalling 19       528_at   up   0.075153984   heat shock 27 kDa protein 3       36224_g_at   down   0.075175637   splicing factor proline/glutamine rich (polypyrimidine tract binding                   protein associated)       33194_at   up   0.07528018   RCD1 required for cell differentiation1 homolog ( S. pombe )       38990_at   down   0.075291777   F-box only protein 9       901_g_at   up   0.075464454   phospholipase C, beta 4       37962_r_at   down   0.07548297   syntaxin binding protein 3       34445_at   down   0.075645748   KIAA0471 gene product       40051_at   up   0.075647797   translocation associated membrane protein 2       34391_at   down   0.07567032   immunoglobulin (CD79A) binding protein 1       40151_s_at   down   0.075685419   peroxisome receptor 1       32183_at   down   0.075709577   splicing factor, arginine/serine-rich 11       40024_at   up   0.075728682   src homology three (SH3) and cysteine rich domain       34611_at   up   0.075745185   zinc finger protein 192       35590_s_at   up   0.075756397   gastric inhibitory polypeptide receptor       38637_at   up   0.075790154   lysyl oxidase       36114_r_at   up   0.07582013   troponin T1, skeletal, slow       39017_at   down   0.075913788   LSM1 homolog, U6 small nuclear RNA associated ( S. cerevisiae )       40947_at   up   0.075914155   hypothetical protein FLJ12671       39782_at   down   0.075915309   nuclear DNA-binding protein       1845_at   down   0.075997345   mitogen-activated protein kinase kinase 4       36145_at   up   0.076021749   fuse-binding protein-interacting repressor       32958_at   down   0.076024781   G protein-coupled receptor, family C, group 5, member B       41131_f_at   down   0.076033961   heterogeneous nuclear ribonucleoprotein H2 (H′)       40516_at   down   0.076092957   aryl hydrocarbon receptor       35161_at   up   0.07609887   likely ortholog of mouse ubiquitin conjugating enzyme 7 interactin                   protein 5       38656_s_at   down   0.076198725   hypothetical protein MGC5576       34869_at   up   0.076217032   LIM domain binding 3       40982_at   down   0.076234385   hypothetical protein FLJ10534       36364_at   up   0.07623929   4-aminobutyrate aminotransferase       35751_at   down   0.076289997   succinate dehydrogenase complex, subunit B, iron sulfur (Ip)       34907_at   up   0.076316825   apoptosis-associated tyrosine kinase       33111_at   up   0.076325246   natural killer cell receptor, immunoglobulin superfamily member       1500_at   up   0.076347224   Wilms tumor 1       41155_at   down   0.076354576   catenin (cadherin-associated protein), alpha 1, 102 kDa       39107_at   up   0.076418762   lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)       41815_at   down   0.076423878   spectrin repeat containing, nuclear envelope 2       33382_at   down   0.076464267   N-acylsphingosine amidohydrolase (acid ceramidase)-like       690_s_at   up   0.076507955   kinase insert domain receptor (a type III receptor tyrosine kinase)       38699_at   up   0.076517467   tubulin, beta, 5       32315_at   down   0.076580486   ribosomal protein S24       32394_s_at   down   0.076586658   ribosomal protein L23       1323_at   down   0.076619803   ubiquitin B       520_at   up   0.076637949   mitogen-activated protein kinase kinase kinase 12       31977_at   up   0.076645346   guanylate cyclase 2D, membrane (retina-specific)       40874_at   down   0.076645607   endothelial differentiation-related factor 1       41474_at   down   0.076668881   kinesin heavy chain member 2       1508_at   up   0.076750896   integrin, alpha 9       41252_s_at   down   0.07680594   chorionic somatomammotropin hormone 2       35449_at   down   0.076867169   killer cell lectin-like receptor subfamily B, member 1       38478_at   up   0.07688698   splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot                   homolog,  Drosophila )       33188_at   up   0.076919217   peptidylprolyl isomerase (cyclophilin)-like 2       41753_at   up   0.076936025   actinin, alpha 4       35309_at   up   0.076946588   suppression of tumorigenicity 14 (colon carcinoma, matriptase,                   epithin)       41586_at   up   0.076953724   fibroblast growth factor 18       33729_at   down   0.076996832   solute carrier family 25 (mitochondrial carrier, brain), member 14       37448_s_at   down   0.07699865   GNAS complex locus       2084_s_at   up   0.077059452   ets variant gene 4 (E1A enhancer binding protein, E1AF)       35118_at   up   0.077061841   lecithin-cholesterol acyltransferase       40327_at   up   0.077082465   homeo box B13       38244_at   up   0.077091148   hypothetical protein FLJ10178       32853_at   down   0.077112143   translocase of outer mitochondrial membrane 70 homolog A                   (yeast)       38726_at   up   0.077113456   dolichyl-phosphate mannosyltransferase polypeptide 2, regulatory                   subunit       32219_at   down   0.077119778   tousled-like kinase 1       39555_at   down   0.077128151   inhibitor of growth family, member 1-like       35518_at   up   0.07719372   protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen                   and sarcoplasmic reticulum binding subunit, skeletal muscle)       39494_at   up   0.07720618       37023_at   down   0.077401057   lymphocyte cytosolic protein 1 (L-plastin)       41859_at   up   0.077419258   uronyl-2-sulfotransferase       40543_at   up   0.077431976   achaete-scute complex-like 1 ( Drosophila )       1232_s_at   up   0.077484241   insulin-like growth factor binding protein 1       41199_s_at   down   0.07749603   splicing factor proline/glutamine rich (polypyrimidine tract binding                   protein associated)       32300_s_at   up   0.077509791   tyrosine hydroxylase       41546_at   up   0.077594704   cyclin-dependent kinase 6       40044_at   up   0.077618336   ELL gene (11-19 lysine-rich leukemia gene)       34372_at   down   0.077632667   upstream regulatory element binding protein 1       32379_f_at   up   0.07769327   pyruvate kinase, muscle       31475_at   up   0.07772506   tankyrase, TRF1-interacting ankyrin-related ADP-ribose                   polymerase       35322_at   down   0.077745028   Kelch-like ECH-associated protein 1       33741_at   down   0.077773426   ATPase, H+ transporting, lysosomal 50/57 kDa, V1 subunit H       36207_at   down   0.077808208   SEC14-like 1 ( S. cerevisiae )       39504_at   up   0.077809572   gap junction protein, alpha 12, 47 kDa       35946_at   up   0.077814129   NEL-like 1 (chicken)       39303_at   up   0.077857901   beta-transducin repeat containing       34946_at   down   0.077936804   immunoglobulin superfamily, member 6       34628_at   up   0.07797503   TAF4b RNA polymerase II, TATA box binding protein (TBP)-                   associated factor, 105 kDa       38045_at   up   0.077978903   catenin (cadherin-associated protein), delta 2 (neural plakophilin-                   related arm-repeat protein)       38392_at   down   0.077981436   actin related protein 2/3 complex, subunit 5, 16 kDa       41825_at   up   0.077994663   PTEN induced putative kinase 1       31333_at   up   0.078003393   tolloid-like 1       34686_at   up   0.078059255   adenylate cyclase 2 (brain)       34269_at   down   0.078146471   erythroid differentiation-related factor 1       37725_at   down   0.078156806   protein phosphatase 1, catalytic subunit, gamma isoform       1266_s_at   up   0.078163951   lymphocyte-specific protein tyrosine kinase       1616_at   up   0.078185303   fibroblast growth factor 9 (glia-activating factor)       37563_at   up   0.078201931   SLIT-ROBO Rho GTPase activating protein 2       39336_at   up   0.078228671   ADP-ribosylation factor 3       33698_at   up   0.07823379   KIAA1052 protein       31408_at   up   0.07830084   retinal pigment epithelium-derived rhodopsin homolog       38900_at   up   0.078345513   paired box gene 3 (Waardenburg syndrome 1)       32983_at   up   0.078360832   adrenergic, alpha-1B-, receptor       32252_at   up   0.078369125   transthyretin (prealbumin, amyloidosis type I)       32675_at   down   0.078370483   bone marrow stromal cell antigen 1       1058_at   down   0.07837205   WAS protein family, member 3       34915_at   up   0.078441436   solute carrier family 8 (sodium/calcium exchanger), member 1       41506_at   down   0.078473991   mitogen-activated protein kinase-activated protein kinase 5       160028_s_at   up   0.078607486   ret proto-oncogene (multiple endocrine neoplasia and medullary                   thyroid carcinoma 1, Hirschsprung disease)       1085_s_at   down   0.07863644   phospholipase C, gamma 2 (phosphatidylinositol-specific)       36471_f_at   up   0.078683795   dystrobrevin, alpha       34873_at   up   0.078715546   nebulette       37045_at   down   0.078754743   sorting nexin 19       1682_s_at   up   0.078774726   ATP-binding cassette, sub-family B (MDR/TAP), member 1       557_s_at   up   0.078820073   somatostatin receptor 3       41853_at   down   0.078881429   phosphoribosyl pyrophosphate synthetase-associated protein 2       1207_at   up   0.078910905   cyclin-dependent kinase 6       36228_at   up   0.078961242   glycine-N-acyltransferase       1776_at   up   0.079007645   Ras-related associated with diabetes       39653_at   up   0.079043266   protection of telomeres 1       1652_at   up   0.079084497   pim-2 oncogene       969_s_at   down   0.079111129   ubiquitin specific protease 9, X chromosome (fat facets-like                     Drosophila )       33847_s_at   down   0.079127006   cyclin-dependent kinase inhibitor 1B (p27, Kip1)       32073_at   down   0.07922512   KIAA0677 gene product       31403_at   up   0.079247982   solute carrier family 18 (vesicular monoamine), member 1       32776_at   down   0.079253268   v-ral simian leukemia viral oncogene homolog B (ras related; GTP                   binding protein)       40585_at   down   0.079269329   adenylate cyclase 7       36696_at   up   0.079410568   phosphatidylinositol glycan, class C, pseudogene 1       1921_at   up   0.079426983       40377_at   up   0.079435641   KIAA0682 gene product       32916_at   down   0.079476859   protein tyrosine phosphatase, receptor type, E       39444_at   down   0.079505682   splicing factor 3b, subunit 1, 155 kDa       32160_at   down   0.079628498   seven in absentia homolog 1 ( Drosophila )       33929_at   up   0.079641537   glypican 1       379_at   down   0.079657938   ATP binding protein associated with cell differentiation       31862_at   up   0.07967263   wingless-type MMTV integration site family, member 5A       33027_at   up   0.079685137       36641_at   down   0.079685686   capping protein (actin filament) muscle Z-line, alpha 2       36703_at   up   0.079773179   chemokine (C—C motif) ligand 25       32447_at   up   0.079824503   nuclear receptor subfamily 5, group A, member 1       39449_at   up   0.079834205   S-phase kinase-associated protein 2 (p45)       39057_at   up   0.079838689   kinesin 2 60/70 kDa       32792_at   down   0.07988668   GCIP-interacting protein p29       31461_at   up   0.079924048   proteasome (prosome, macropain) 26S subunit, non-ATPase, 4,                   pseudogene       38801_at   down   0.079926213   VAMP (vesicle-associated membrane protein)-associated protein                   A, 33 kDa       1018_at   up   0.079992699   wingless-type MMTV integration site family, member 10B       37646_at   down   0.079999644   polymerase (DNA directed), delta 3       40093_at   up   0.080005061   Lutheran blood group (Auberger b antigen included)       41855_at   down   0.080076262   histone acetyltransferase 1       40116_at   up   0.080078498   phosphofructokinase, liver       40483_at   up   0.080102456   transcriptional activator of the c-fos promoter       37214_g_at   down   0.080139379   deoxyribonuclease I-like 1       1975_s_at   up   0.080172198   insulin-like growth factor 1 (somatomedin C)       32653_at   up   0.080182256   bromodomain containing 8       33375_at   up   0.080187989   myosin VI       37632_s_at   down   0.080207214   zuotin related factor 1       37353_g_at   down   0.080208739   nuclear antigen Sp100       AFFX-BioB-5_at   up   0.080316663       34529_at   up   0.080325324       31459_i_at   up   0.080332933   immunoglobulin lambda locus       35524_at   up   0.080365829   complement component 8, gamma polypeptide       37144_at   up   0.080399764   protein inhibitor of activated STAT protein PIASy       33312_at   down   0.080410486   crystallin, alpha A       37278_at   up   0.080412116   tafazzin (cardiomyopathy, dilated 3A (X-linked); endocardial                   fibroelastosis 2; Barth syndrome)       35973_at   down   0.080418152   huntingtin interacting protein 14       38469_at   up   0.080430213   transmembrane 4 superfamily member 3       35218_at   down   0.080433054   programmed cell death 10       38750_at   up   0.080450803   Notch homolog 3 ( Drosophila )       38396_at   up   0.080454362       37493_at   down   0.080471928   colony stimulating factor 2 receptor, beta, low-affinity (granulocyte                   macrophage)       38024_at   up   0.080480542   rap2 interacting protein x       34300_at   down   0.080530264   zinc finger protein 278       32367_at   down   0.080576466   signal-regulatory protein beta 1       32504_at   down   0.080592308   sorting nexin 27       1452_at   down   0.080634481   LIM domain only 4       33859_at   down   0.080676216   sin3-associated polypeptide, 18 kDa       34462_at   up   0.080685447   sodium channel, nonvoltage-gated 1, delta       34653_at   up   0.080686415   receptor-associated protein of the synapse, 43 kD       33466_at   up   0.080709789   hypothetical gene supported by AF038182; BC009203       33880_at   up   0.080756283   fatty-acid-Coenzyme A ligase, long-chain 3       1504_s_at   up   0.080866712   fibroblast growth factor 12       41245_at   up   0.080874178   growth differentiation factor 10       1220_g_at   up   0.080887   interferon regulatory factor 2       38411_at   down   0.080931281       32017_at   up   0.08094505   par-6 partitioning defective 6 homolog beta (C. elegans)       38581_at   down   0.080999597   guanine nucleotide binding protein (G protein), q polypeptide       32615_at   down   0.081013831   aspartyl-tRNA synthetase       35206_at   up   0.081072588   centrosomal protein 2       2083_at   up   0.081109896   cholecystokinin B receptor       35183_at   up   0.081139697   ATP-binding cassette, sub-family A (ABC1), member 3       39337_at   down   0.081179863   H2A histone family, member Z       32805_at   up   0.081185775   aido-keto reductase family 1, member C2 (dihydrodiol                   dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid                   dehydrogenase, type III)       39287_at   up   0.081237036       35213_at   up   0.081275089   WW domain binding protein 4 (formin binding protein 21)       32090_at   up   0.081301613   nicotinamide nucleotide adenylyltransferase 2       39661_s_at   up   0.081331131   solute carrier family 29 (nucleoside transporters), member 2       41163_at   down   0.081429809   integral type I protein       37382_at   up   0.081475975   ribosomal protein S26       31932_f_at   down   0.0814765   basic transcription factor 3       31354_r_at   up   0.081482365   forkhead box E2       33771_at   up   0.081500647   T-cell activation leucine repeat-rich protein       40994_at   up   0.08156926   G protein-coupled receptor kinase 5       41219_at   down   0.081589471   KIAA0570 gene product       38349_at   down   0.081612444   itchy homolog E3 ubiquitin protein ligase (mouse)       35767_at   down   0.081661911   GABA(A) receptor-associated protein-like 2       1894_f_at   up   0.08166614       41846_at   up   0.081743099   cone-rod homeobox       38082_at   down   0.081774309   KIAA0650 protein       39581_at   down   0.081796001   cystatin A (stefin A)       38566_at   up   0.081805999   collagen, type X, alpha 1(Schmid metaphyseal chondrodysplasia)       35378_at   up   0.081840606   luteinizing hormone beta polypeptide       39788_at   down   0.081846683   plakophilin 4       40358_at   up   0.081926303   GLI-Kruppel family member GLI3 (Greig cephalopolysyndactyly                   syndrome)       35980_at   up   0.081980276   phospholipase C, beta 1 (phosphoinositide-specific)       1790_s_at   up   0.081983581       35916_s_at   down   0.082014903   heterogeneous nuclear ribonucleoprotein A3       39611_at   up   0.082030651       32876_s_at   up   0.082062451   rhodopsin (opsin 2, rod pigment) (retinitis pigmentosa 4,                   autosomal dominant)       35754_at   down   0.082097137   transmembrane trafficking protein       32574_at   up   0.082104017   sphingomyelin phosphodiesterase 1, acid lysosomal (acid                   sphingomyelinase)       41565_at   up   0.08210775   ataxin 2 related protein       31340_at   up   0.082177875   matrix metalloproteinase 20 (enamelysin)       219_i_at   up   0.08227682   microtubule-associated protein 2       32968_s_at   up   0.082355877   seizure related 6 homolog (mouse)-like       41212_r_at   down   0.082413942   Williams-Beuren syndrome chromosome region 1       38824_at   down   0.082607893   HIV-1 Tat interactive protein 2, 30 kDa       38134_at   down   0.082648743   pleiomorphic adenoma gene 1       1128_s_at   up   0.082677345   chemokine (C—C motif) receptor 1       31393_r_at   up   0.082784321   undifferentiated embryonic cell transcription factor 1       1521_at   down   0.08282553   non-metastatic cells 1, protein (NM23A) expressed in       37523_at   up   0.082918602   acyl-Coenzyme A dehydrogenase, long chain       32244_at   down   0.082923664   chromosome 14 open reading frame 92       38845_at   up   0.082976532   pyruvate dehydrogenase kinase, isoenzyme 2       39759_at   down   0.082990311   quaking homolog, KH domain RNA binding (mouse)       1742_at   up   0.082991136   v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian)       39817_s_at   up   0.083028753   putative c-Myc-responsive       36510_at   down   0.083073712   general transcription factor IIF, polypeptide 2, 30 kDa       38087_s_at   down   0.083134517   S100 calcium binding protein A4 (calcium protein, calvasculin,                   metastasin, murine placental homolog)       188_at   up   0.083158625   ephrin-B1       32400_at   up   0.083178012   myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog,                     Drosophila ); translocated to, 1       36753_at   down   0.083213097   leukocyte immunoglobulin-like receptor, subfamily B (with TM and                   ITIM domains), member 4       37635_at   up   0.083222309   trichohyalin       39268_at   down   0.083225995   potassium voltage-gated channel, subfamily F, member 1       40586_at   up   0.08323434   eukaryotic translation elongation factor 1 epsilon 1       39452_s_at   up   0.083253328   spectrin, beta, non-erythrocytic 1       31563_at   up   0.083296186       37681_i_at   up   0.083326759   matrin 3       37426_at   up   0.083400663   trinucleotide repeat containing 9       40286_r_at   up   0.08342016       39524_at   up   0.08346012   rhodopsin (opsin 2, rod pigment) (retinitis pigmentosa 4,                   autosomal dominant)       1668_s_at   down   0.08347108   von Hippel-Lindau syndrome       835_at   up   0.083523429   PDGFA associated protein 1       37661_at   down   0.083561216   ATPase, Ca++ transporting, plasma membrane 1       35702_at   up   0.083576593   hydroxysteroid (11-beta) dehydrogenase 1       32460_at   up   0.083625268   gamma-aminobutyric acid (GABA) A receptor, beta 2       40732_at   down   0.083646527   nuclear protein, ataxia-telangiectasia locus       32276_at   down   0.083660424   ribosomal protein L32       35652_g_at   down   0.083671345   mitogen-activated protein kinase kinase kinase 4       41429_at   up   0.083680874   protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65)                   beta isoform       33994_g_at   up   0.083688844   myosin, light polypeptide 6, alkali, smooth muscle and non-muscle       38284_at   up   0.083709948   myeloid/lymphoid or mixed-lineage leukemia 4       40592_at   up   0.08373631   iduronate 2-sulfatase (Hunter syndrome)       39519_at   down   0.083740037   KIAA0692 protein       37871_at   up   0.083797679   islet amyloid polypeptide       38635_at   down   0.083816871   signal sequence receptor, delta (translocon-associated protein                   delta)       40246_at   down   0.083844581   discs, large ( Drosophila ) homolog 1       33948_at   up   0.083864694   corticotropin releasing hormone receptor 2       36087_at   up   0.083865581   KIAA0409 protein       515_s_at   up   0.083916267   Cas-Br-M (murine) ecotropic retroviral transforming sequence b       38948_at   up   0.083927389   protein phosphatase 1, regulatory subunit 3D       32500_at   up   0.083952172       1450_g_at   down   0.083974175   proteasome (prosome, macropain) subunit, alpha type, 4       34469_at   up   0.084001125   ABO blood group (transferase A, alpha 1-3-N-                   acetylgalactosaminyltransferase; transferase B, alpha 1-3-                   galactosyltransferase)       39010_at   down   0.084111642   endosulfine alpha       38409_at   down   0.084142918   sperm specific antigen 2       33237_at   down   0.084175575   RNA helicase       31502_at   up   0.084292511   annexin A2       559_s_at   up   0.084353486   T-cell leukemia, homeobox 1       34760_at   down   0.08437959   C-type lectin BIMLEC precursor       1464_at   up   0.084410452       38295_at   down   0.084421315   pre-B-cell leukemia transcription factor 2       40318_at   up   0.084546986   dynein, cytoplasmic, intermediate polypeptide 1       38350_f_at   down   0.084601034   tubulin, alpha 2       41870_at   up   0.084650654   lung type-I cell membrane-associated glycoprotein       32058_at   up   0.084659847   carbohydrate sulfotransferase 10       36994_at   up   0.084686096   ATPase, H+ transporting, lysosomal 16 kDa, V0 subunit c       38681_at   down   0.084759916   eukaryotic translation initiation factor 3, subunit 6 48 kDa       1069_at   down   0.08476962   prostaglandin-endoperoxide synthase 2 (prostaglandin G/H                   synthase and cyclooxygenase)       40407_at   down   0.084769798   karyopherin alpha 2 (RAG cohort 1, importin alpha 1)       36986_at   up   0.084799441   lysophospholipase II       36102_at   down   0.084832731   voltage-dependent anion channel 3       38972_at   down   0.08489681   hypothetical protein BC013764       1854_at   up   0.084942696   v-myb myeloblastosis viral oncogene homolog (avian)-like 2       32152_at   up   0.084966808   ankyrin 1, erythrocytic       31968_at   up   0.084975489       39673_i_at   up   0.084986743   extracellular matrix protein 2, female organ and adipocyte specific       1441_s_at   down   0.085018907   tumor necrosis factor receptor superfamily, member 6       38619_at   up   0.085083592   golgl SNAP receptor complex member 2       37138_at   up   0.085132288   KIAA0809 protein       39793_at   down   0.085149958   glioblastoma amplified sequence       1060_g_at   up   0.085200706   neurotrophic tyrosine kinase, receptor, type 3       36647_at   down   0.085228019   hypothetical protein FLJ10326       40155_at   down   0.085237267   actin binding LIM protein 1       36538_at   up   0.085374834   protein phosphatase 1, regulatory (inhibitor) subunit 13B       41405_at   up   0.08539692   secreted frizzled-related protein 4       33842_at   up   0.085425991   hypothetical protein FLJ11560       644_at   up   0.085440532   ras homolog gene family, member N       1615_at   up   0.085579584   BCL2-like 1       40102_at   down   0.08561703   oxysterol binding protein-like 2       40824_at   down   0.085638027   exportin 7       37820_at   up   0.085679373   proline dehydrogenase (oxidase) 2       36310_at   up   0.085731979   keratin, hair, acidic, 1       1935_at   up   0.085805182   Mdm4, transformed 3T3 cell double minute 4, p53 binding protein                   (mouse)       40218_at   up   0.085816577   CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 1       33201_at   up   0.085854381   lethal giant larvae homolog 1 ( Drosophila )       34439_at   up   0.085866067   absent in melanoma 2       40210_at   down   0.086009164   RAB13, member RAS oncogene family       41768_at   down   0.086063925   protein kinase, cAMP-dependent, regulatory, type I, alpha (tissue                   specific extinguisher 1)       33089_s_at   down   0.08610984   ephrin-A2       33914_r_at   up   0.086112896   ferrochelatase (protoporphyria)       35512_at   up   0.086129344       37951_at   up   0.086142772   deleted in liver cancer 1       40033_at   up   0.086265844   mitogen-activated protein kinase 11       40801_at   down   0.08636791   DKFZP434C212 protein       41662_at   down   0.086379918   DKFZP566B183 protein       40437_at   down   0.086444658   DKFZP564G2022 protein       34326_at   down   0.08654165   coatomer protein complex, subunit beta       38924_s_at   down   0.086590576   spectrin SH3 domain binding protein 1       39721_s_at   up   0.086598108   ephrin-B1       36283_at   up   0.086609599   DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 6 (RNA helicase                   54 kDa)       41125_r_at   up   0.086618972   ectonucleotide pyrophosphatase/phosphodiesterase 2 (autotaxin)       38985_at   down   0.086620716   leptin receptor overlapping transcript-like 1       33705_at   down   0.086752173   phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4                   dunce homolog,  Drosophila )       33378_at   down   0.086759624   IDN3 protein       37706_at   up   0.086771534   golgi apparatus protein 1       40126_at   up   0.086915064   paired mesoderm homeo box 1       38040_at   down   0.086916527   splicing factor 30, survival of motor neuron-related       1711_at   up   0.086923062   tumor protein p53 binding protein, 1       1317_at   up   0.086948161   macrophage stimulating 1 receptor (c-met-related tyrosine kinase)       38403_at   down   0.086971119   lysosomal-associated membrane protein 2       33657_at   down   0.086989849   ribosomal protein L34       36537_at   down   0.087068338   Rho-specific guanine nucleotide exchange factor p114       37027_at   down   0.087167604   AHNAK nucleoprotein (desmoyokin)       1149_at   down   0.087172748       34725_at   up   0.087190996   glucocorticoid receptor DNA binding factor 1       38035_at   down   0.087230646   myotubularin related protein 6       1489_s_at   up   0.087275505   v-myc myelocytomatosis viral oncogene homolog 1, lung                   carcinoma derived (avian)       340_at   up   0.087320254   matrilin 3       521_at   up   0.087361038   metallothionein IV       39717_g_at   down   0.087391993   mitochondrial ribosomal protein L33       40633_at   up   0.087439293   mitotic control protein dis3 homolog       36165_at   down   0.087457854   cytochrome c oxidase subunit VIc       31735_at   up   0.087477585   type 1 protein phosphatase inhibitor       31417_at   up   0.087483514   hypocretin (orexin) neuropeptide precursor       38062_at   up   0.087507618   guanine nucleotide exchange factor for Rap1       38106_at   down   0.087527635   TGF beta-inducible nuclear protein 1       34272_at   up   0.087592461   regulator of G-protein signalling 4       34225_at   up   0.087596552   Wolf-Hirschhorn syndrome candidate 2       41712_at   down   0.087689972   likely ortholog of mouse aquarius       378_s_at   up   0.087796914   GPI anchored molecule like protein       31981_at   up   0.087831344   crystallin, beta B3       899_at   up   0.087862483   Indian hedgehog homolog ( Drosophila )       40933_f_at   up   0.087878586   zinc finger, DHHC domain containing 18       32590_at   down   0.087886008   nucleolin       1397_at   down   0.088027982   mitogen-activated protein kinase kinase kinase 11       38821_at   down   0.088036116   progesterone receptor membrane component 2       41185_f_at   down   0.088044825   SMT3 suppressor of mif two 3 homolog 2 (yeast)       40384_at   up   0.088045667   nephronophthisis 1 (juvenile)       39019_at   down   0.088056769   lysosomal-associated protein transmembrane 4 alpha       676_g_at   up   0.088222263   interferon induced transmembrane protein 1 (9-27)       41389_s_at   up   0.088364655   renal tumor antigen       239_at   down   0.08844228   cathepsin D (lysosomal aspartyl protease)       1842_at   down   0.088450446       34134_at   up   0.088462035       36885_at   down   0.08846417   spleen tyrosine kinase       39489_g_at   up   0.088500732   protocadherin 9       35857_at   up   0.088519565   glutamate receptor, ionotropic, kainate 1       37639_at   up   0.088520319   hepsin (transmembrane protease, serine 1)       AFFX-   up   0.088539866   transferrin receptor (p90, CD71)       HUMTFRR/M11507_5_at       35367_at   down   0.088573711   lectin, galactoside-binding, soluble, 3 (galectin 3)       35957_at   down   0.088641618   stannin       31458_at   up   0.088655659   cytokeratin 2       33192_g_at   down   0.08877997   chromosome 10 open reading frame 6       36523_at   down   0.0887804   ATPase, Cu++ transporting, alpha polypeptide (Menkes                   syndrome)       32658_at   up   0.08879375   SAC2 suppressor of actin mutations 2-like (yeast)       36547_r_at   up   0.088847765   KIAA0542 gene product       32866_at   up   0.08900188   KIAA0605 gene product       36336_s_at   up   0.089108577   KIAA0963 protein       38031_at   down   0.089210079   KIAA0111 gene product       32771_at   up   0.089236711   group-specific component (vitamin D binding protein)       33368_at   down   0.089256532   protease, serine, 15       34441_at   up   0.089294655       38258_at   up   0.089315852       34143_at   up   0.089329234   cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)       39199_at   up   0.08937154       37034_at   down   0.089374662   acidic (leucine-rich) nuclear phosphoprotein 32 family, member A       578_at   up   0.089382491   recombination activating gene 2       35866_at   down   0.089442342   zinc finger protein 268       551_at   down   0.089610262   E1A binding protein p300       32003_at   up   0.089725235   methionine adenosyltransferase I, alpha       1541_f_at   up   0.089862891   interferon, alpha 6       39466_s_at   up   0.089866338       324_f_at   down   0.089873012       41310_f_at   up   0.089892054   nuclear receptor subfamily 2, group F, member 6       41808_at   down   0.090154156   cyclin D binding myb-like transcription factor 1       33037_at   up   0.090155577   carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 7       31466_at   up   0.090205249   major histocompatibility complex, class II, DR beta 6                   (pseudogene)       37323_r_at   up   0.090262072   hydroxyprostaglandin dehydrogenase 15-(NAD)       2091_at   up   0.090282876   wingless-type MMTV integration site family, member 4       32477_at   up   0.090315491   calpain 9 (nCL-4)       34832_s_at   up   0.090482967   KIAA0763 gene product       AFFX-PheX-5_at   up   0.090493351       39141_at   up   0.090696236   ATP-binding cassette, sub-family F (GCN20), member 1       38402_at   down   0.090789867   lysosomal-associated membrane protein 2       34109_at   up   0.090803494   proline dehydrogenase (oxidase) 1       40440_at   up   0.090928291   PAI-1 mRNA-binding protein       34387_at   down   0.091050579   KIAA0205 gene product       40639_at   up   0.09105652   SCO cytochrome oxidase deficient homolog 2 (yeast)       33289_f_at   down   0.091058   zinc finger protein 263       41476_at   up   0.091067637       35661_g_at   up   0.091173127   S-antigen; retina and pineal gland (arrestin)       39959_at   up   0.091197187   ubiquitin D       35129_at   up   0.091246944   sperm adhesion molecule 1 (PH-20 hyaluronidase, zona pellucida                   binding)       1879_at   down   0.091260491   related RAS viral (r-ras) oncogene homolog       37734_at   down   0.091272658   disco-interacting protein 2 ( Drosophila ) homolog       39680_at   up   0.09128097   statherin       1300_at   up   0.091302081   X-ray repair complementing defective repair in Chinese hamster                   cells 2       35494_at   up   0.091514972       AFFX-DapX-3_at   up   0.091526914       35159_at   up   0.091541071   tubulin-specific chaperone e       1686_g_at   down   0.091586384   S-phase response (cyclin-related)       38243_at   up   0.091608235   neural cell adhesion molecule 1       41772_at   up   0.091636193   monoamine oxidase A       36468_at   up   0.091669779   dystrobrevin, alpha       31912_at   up   0.091687981   forkhead box H1       1966_i_at   up   0.091745212   nitric oxide synthase 2C       32392_s_at   up   0.091772778   UDP glycosyltransferase 1 family, polypeptide A4       40854_at   down   0.091958912   ubiquinol-cytochrome c reductase core protein II       37326_at   down   0.091968595   proteolipid protein 2 (colonic epithelium-enriched)       33835_at   up   0.092020494   KIAA0721 protein       32666_at   up   0.092098111   chemokine (C—X—C motif) ligand 12 (stromal cell-derived factor 1)       34101_at   up   0.092129007       33792_at   up   0.092178872   prostate stem cell antigen       38008_at   up   0.092208168   DNA segment on chromosome 4 (unique) 234 expressed                   sequence       33103_s_at   down   0.092213362   adducin 3 (gamma)       1448_at   down   0.092287738   proteasome (prosome, macropain) subunit, alpha type, 3       36213_at   up   0.092306281   malignant fibrous histiocytoma amplified sequence 1       37677_at   down   0.092335261   phosphoglycerate kinase 1       40374_at   up   0.092357025   cardiac ankyrin repeat protein       34264_at   up   0.092400894   RUN and SH3 domain containing 1       36925_at   up   0.092424153   heat shock 70 kDa protein 2       39003_at   down   0.092431788   pituitary tumor-transforming 1 interacting protein       41795_at   down   0.09245412   NCK adaptor protein 1       31906_at   down   0.092499322   heat shock factor binding protein 1       34188_at   down   0.092551592       38019_at   up   0.092684992   casein kinase 1, epsilon       38673_s_at   down   0.092735744   cyclin-dependent kinase inhibitor 1C (p57, Kip2)       34814_at   down   0.092753688   SUMO-1 activating enzyme subunit 2       38212_at   up   0.092799885   UDP-N-acetyl-alpha-D-galactosamine: (N-acetylneuraminyl)-                   galactosylglucosylceramide N-acetylgalactosaminyltransferase                   (GalNAc-T)       31379_at   up   0.092814218   HFSE-1 protein       34578_at   up   0.092823397   sarcoglycan, gamma (35 kDa dystrophin-associated glycoprotein)       41545_at   up   0.092876791   cyclin-dependent kinase 6       38037_at   up   0.092905054   diphtheria toxin receptor (heparin-binding epidermal growth factor-                   like growth factor)       41788_i_at   down   0.092989382   KIAA0669 gene product       32624_at   down   0.093011872   likely ortholog of mouse tuberin-like protein 1       34122_at   up   0.093042118   casein beta       36553_at   down   0.093052406   acetylserotonin O-methyltransferase-like       32679_at   up   0.093083461   likely ortholog of chicken chondrocyte protein with a poly-proline                   region       37117_at   up   0.093191269   Rho GTPase activating protein 8       36077_at   down   0.093212186   RAB, member of RAS oncogene family-like 4       38854_at   up   0.093242092   KIAA0635 gene product       34118_at   up   0.093250389   ATPase, Na+/K+ transporting, beta 2 polypeptide       36414_s_at   down   0.093282245   calcium/calmodulin-dependent serine protein kinase (MAGUK                   family)       32094_at   up   0.093290429   carbohydrate (chondroitin 6) sulfotransferase 3       41137_at   up   0.093310928   protein phosphatase 1, regulatory (inhibitor) subunit 12B       41149_at   up   0.093394734   exonuclease NEF-sp       35268_at   down   0.093406671   axotrophin       33352_at   down   0.093411658   histone 2, H2be       31463_s_at   down   0.093412524       38190_r_at   up   0.093548584   KIAA0645 gene product       40864_at   down   0.093610502   ras-related C3 botulinum toxin substrate 1 (rho family, small GTP                   binding protein Rac1)       40903_at   down   0.093640616   ATPase, H+ transporting, lysosomal interacting protein 2       31874_at   down   0.093647357   growth arrest-specific 2 like 1       33820_g_at   down   0.093671525   lactate dehydrogenase B       35311_at   down   0.093773374   cellular repressor of E1A-stimulated genes       36350_at   up   0.093885805       39663_at   down   0.093917507   mannosidase, alpha, class 2A, member 1       35149_at   up   0.093949795   tumor necrosis factor receptor superfamily, member 5       38451_at   down   0.093966652   ubiquinol-cytochrome c reductase (6.4 kD) subunit       31330_at   down   0.093994243   ribosomal protein S19       34329_at   down   0.094055721   p21 (CDKN1A)-activated kinase 2       40919_at   up   0.094079635   somatostatin receptor 2       41215_s_at   down   0.094096263   inhibitor of DNA binding 2, dominant negative helix-loop-helix                   protein       31901_at   up   0.094118872   potassium voltage-gated channel, shaker-related subfamily, beta                   member 2       1081_at   down   0.094220232   ornithine decarboxylase 1       41194_at   down   0.094258686   signal recognition particle 14 kDa (homologous Alu RNA binding                   protein)       37098_at   up   0.09434038   protoporphyrinogen oxidase       39056_at   down   0.094461372   phosphoribosylaminoimidazole carboxylase,                   phosphoribosylaminoimidazole succinocarboxamide synthetase       37527_at   up   0.094565974   ELK3, ETS-domain protein (SRF accessory protein 2)       35998_at   up   0.094588743       35328_at   up   0.094596866       31815_r_at   up   0.094601451   low density lipoprotein receptor-related protein 3       34282_at   down   0.094675793   nuclear factor (erythroid-derived 2)-like 3       36463_at   down   0.094675835   BCL2-associated athanogene 5       37679_at   down   0.094863772   interferon-related developmental regulator 1       34062_at   up   0.094905599   ets variant gene 2       40080_at   up   0.094934258   KIAA0090 protein       41414_at   up   0.094942383   chromosome 22 open reading frame 3       40977_f_at   up   0.095014531   cerebellar degeneration-related protein 1, 34 kDa       35897_r_at   up   0.095044456   brain-specific angiogenesis inhibitor 1       1428_at   down   0.095078801       37773_at   up   0.095087394   KIAA1005 protein       40431_at   down   0.095109067   KIAA0431 protein       36203_at   down   0.095163871   ornithine decarboxylase 1       444_g_at   up   0.095292483   homeo box D4       1244_at   up   0.095328326   signal transducer and activator of transcription 2, 113 kDa       39995_s_at   up   0.095391047   WW domain containing oxidoreductase       39178_at   down   0.095462475   reticulon 1       31706_at   up   0.09547677       40023_at   up   0.095557348   brain-derived neurotrophic factor       34472_at   up   0.095594647   frizzled homolog 6 ( Drosophila )       38950_r_at   up   0.095606306   matrix metalloproteinase 23B       1852_at   up   0.095612496   tumor necrosis factor (TNF superfamily, member 2)       41174_at   up   0.095643232   RAN binding protein 2-like 1       34761_r_at   down   0.095664289   a disintegrin and metalloproteinase domain 9 (meltrin gamma)       40449_at   up   0.095715432   replication factor C (activator 1) 1, 145 kDa       35826_at   up   0.095727306   suppressor of Ty 5 homolog ( S. cerevisiae )       700_s_at   up   0.09583438       582_g_at   down   0.095875255   nuclear receptor subfamily 2, group C, member 1       39244_at   down   0.095915812   RAB4A, member RAS oncogene family       32899_s_at   up   0.095919044   RAR-related orphan receptor A       32296_at   up   0.095927535   carbonic anhydrase VA, mitochondrial       36679_at   down   0.095972007   signal recognition particle receptor (‘docking protein’)       31885_at   up   0.095999682   protein tyrosine phosphatase, non-receptor type 3       368_at   up   0.096090928   trophoblast glycoprotein       36313_at   down   0.096111046   ecotropic viral integration site 2A       41367_at   up   0.09615194   hepatocyte nuclear factor 4, gamma       34610_at   down   0.096189258   guanine nucleotide binding protein (G protein), beta polypeptide 2                   like 1       41093_at   up   0.096218086   opioid binding protein/cell adhesion molecule-like       38093_at   down   0.096246266   chromosome 14 open reading frame 32       35345_at   up   0.096248258   3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2                   (mitochondrial)       40976_at   up   0.09628133   katanin p80 (WD repeat containing) subunit B 1       32295_at   up   0.096300607   HLA complex group 9       1636_g_at   up   0.096306453   v-abl Abelson murine leukemia viral oncogene homolog 1       35595_at   up   0.096330447   calcitonin gene-related peptide-receptor component protein       40533_at   up   0.096342646   baculoviral IAP repeat-containing 5 (survivin)       1261_i_at   up   0.096407666   glutathione S-transferase A2       32567_at   up   0.096421885   choline kinase       36100_at   up   0.096473819   vascular endothelial growth factor       40256_at   up   0.09651525       37747_at   down   0.096606126   annexin A5       37764_at   up   0.096642303   holocarboxylase synthetase (biotin-[proprionyl-Coenzyme A-                   carboxylase (ATP-hydrolysing)] ligase)       34613_at   up   0.096690958   KIAA1086 protein       615_s_at   up   0.09674634   parathyroid hormone-like hormone       31827_s_at   up   0.096759998   trans-golgi network protein 2       32011_g_at   up   0.096816474   hypothetical protein EAN57       33086_at   up   0.096895282   prophet of Pit1, paired-like homeodomain transcription factor       34942_at   up   0.097018589   hypothetical protein FLJ38993       39578_at   up   0.097121586   hairless       41460_at   down   0.097154944   RNA binding motif protein 14       31713_s_at   up   0.097197158   discs, large ( Drosophila ) homolog-associated protein 2       32277_at   up   0.097229418   potassium voltage-gated channel, shaker-related subfamily,                   member 3       462_at   up   0.097234978   nuclear factor I/B       35187_at   down   0.097264305       38033_at   up   0.097281795   DKFZP564M1416 protein       464_s_at   down   0.097305326   interferon-induced protein 35       41120_at   up   0.097408034   aminomethyltransferase (glycine cleavage system protein T)       40381_at   up   0.097503532   KIAA0972 protein       41587_g_at   up   0.097533335   fibroblast growth factor 18       39825_at   up   0.097585237   solute carrier family 25 (mitochondrial carrier; citrate transporter),                   member 1       1822_at   up   0.097654682       32178_r_at   down   0.097713503   synaptosomal-associated protein, 23 kDa       1447_at   down   0.097772909   proteasome (prosome, macropain) subunit, beta type, 1       33930_at   down   0.097850141   chromosome 14 open reading frame 163       36353_at   up   0.097867455   hairy and enhancer of split ( Drosophila ) homolog 2       35093_at   up   0.097907561   purinergic receptor P2X-like 1, orphan receptor       1357_at   down   0.09799221   ubiquitin specific protease 4 (proto-oncogene)       37280_at   up   0.098054947   MAD, mothers against decapentaplegic homolog 1 ( Drosophila )       1907_at   up   0.098069395   retinoblastoma-like 1 (p107)       33141_at   up   0.098156986   hydroxysteroid (17-beta) dehydrogenase 1       39686_g_at   down   0.098160911   like mouse brain protein E46       37673_at   down   0.09818696   neutral sphingomyelinase (N-SMase) activation associated factor       38110_at   down   0.098232139   syndecan binding protein (syntenin)       34879_at   down   0.098241379   dolichyl-phosphate mannosyltransferase polypeptide 1, catalytic                   subunit       38609_at   up   0.098269966   sarcoglycan, alpha (50 kDa dystrophin-associated glycoprotein)       37492_at   up   0.098274979   KIAA0500 protein       34100_at   up   0.098277118       37996_s_at   up   0.098280565   dystrophia myotonica-protein kinase       35824_at   down   0.098305072   zinc finger protein 238       40086_at   down   0.098345702   friend of EBNA2       32083_at   down   0.098363125   transmembrane 7 superfamily member 1 (upregulated in kidney)       34977_at   down   0.09838151   sialic acid binding lg-like lectin 7       33161_at   down   0.098418566   hypothetical protein MGC15523       37861_at   up   0.098434036   CD1E antigen, e polypeptide       38784_g_at   up   0.098470912   mucin 1, transmembrane       38020_at   down   0.098546526   KIAA0652 gene product       808_at   up   0.098588848   RAB27B, member RAS oncogene family       1695_at   down   0.098764335   neural precursor cell expressed, developmentally down-regulated 8       36130_f_at   up   0.098794417   metallothionein 1E (functional)       31612_at   up   0.098800032   secretoglobin, family 1D, member 1       37900_at   down   0.099027962   peroxisomal biogenesis factor 11B       33809_at   up   0.099045406   guanine nucleotide binding protein (G protein), alpha inhibiting                   activity polypeptide 1       38722_at   up   0.099099373   collagen, type VI, alpha 1       36522_at   up   0.099155422   mucoepidermoid carcinoma translocated 1       2051_at   up   0.099167839   O-6-methylguanine-DNA methyltransferase       38907_at   up   0.099379332       40860_s_at   up   0.099381562   nuclear protein UKp68       40880_r_at   up   0.099383953   chloride channel 3       41370_at   down   0.099417017   U5 snRNP-specific 40 kDa protein (hPrp8-binding)       36968_s_at   down   0.099572253   Opa-interacting protein 2       32325_at   up   0.099581291       33524_at   up   0.099592485   v-crk sarcoma virus CT10 oncogene homolog (avian)-like       33388_at   up   0.099596344   testis expressed gene 261       35321_at   down   0.099608404   tousled-like kinase 2       36946_at   down   0.099667092   dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A       1348_s_at   down   0.099835885   proplonyl Coenzyme A carboxylase, alpha polypeptide       41737_at   down   0.099885912   serine/arginine repetitive matrix 1       39558_s_at   up   0.099902424       39474_s_at   up   0.099944447   cysteine knot superfamily 1, BMP antagonist 1       38825_at   up   0.099970407   fibrinogen, A alpha polypeptide       38164_at   down   0.099971672   retinitis pigmentosa GTPase regulator                  
 
     Example 3  
     Prostate Tumor Diagnosis Through Bloodcell Multigene Signatures  
     Introduction  
      Prostate cancer is the second largest cancer killer of men in the Unites States and Europe. It has been estimated that in 2000, in the U.S., 180,400 men were diagnosed with prostate cancer and approximately 32,000 died in that year alone (Greenlee et al., CA Cancer J Clin. 2000; 50(1):7-33). Current techniques for the screening and risk assessment of prostate cancer, as a prerequisite to surgical biopsy procedures, are based upon the measurement of either individual serum biomarkers, or expression of individual genes in circulating malignant cells (Oesterling et al., JAMA 1993; 270(7):860-4; Seaman et al., Urol Clin North Am.; 1993; 20(4):653-63; and Catalona et al., Urology 2000; 56(2):255). These techniques, which include RT-PCR, possess a number of limitations, including lack of specificity and accuracy in the diagnosis and, also a lack of prognostic information. This ultimately yields high numbers of false positive diagnoses, and consequently unnecessarily large numbers of surgical biopsies.  
      Since its clinical approval by the FDA in 1986, prostate specific antigen (PSA) has been recognized as the most useful biomarker for diagnosis and surveillance of prostate cancer. In current clinical practice, a serum PSA assay (which quantifies levels of PSA protein as ng/ml in sera prepared from peripheral blood), in conjunction with digital rectal examination (DRE), is used to indicate which patients should undergo prostate biopsy. Prostate cancer statistics have clearly shown that pre-screening prior to biopsy has led to both an increase in the number of men diagnosed with cancer and a decline in age of diagnosis due to earlier detection (Roberts et al., Urology. 2000; 56(5):817-22). It was estimated that during 1997, over 750,000 prostate biopsies were performed following PSA and DRE screening (ref). However, although for example PSA is an effective indicator of prostate cancer when serum levels are high, diagnostic assays based on this marker become more ambiguous when levels are only moderately elevated, i.e. between 2-10 ng/ml. Abnormal findings from DRE have also been attributed to various benign conditions, thus contributing to this low accuracy of cancer detection rates prior to biopsy (Roberts et al., Urology. 2000; 56(5):817-22). A false-positive pre-biopsy diagnosis of cancer has been reported in 40-6% of men with both abnormal DRE and PSA levels greater than 4 ng/ml, resulting in a high percent of unnecessary prostate biopsies (Bangma et al., J Urol. 1997:157(6):2191-6; Smith et al., Cancer. 1997; 80(9):1852-6; Roberts et al., Urology. 2000; 56(5):817-22).  
      Although methods have been investigated to increase specificity of PSA, such as the use of free/total PSA measurements (Catalona et al., Urology 2000; 56(2):255), a recent review of screening programs has suggested that even though the use of free/total PSA serum measurements may reduce the need for biopsy by up to 40%, approximately 12% of all tumors would still be missed with this assay (Neal et al., Eur J Cancer 2000; 36(10):1316-21). In addition, serum quantitation of biomarkers, such as PSA, does not reliably correlate with important cancer variables such as biological aggressiveness, does not allow outcome predictions in patients with hormone refractory disease (Murphy et al et al., Cancer. 1998; 83(11):2259-69), and does not identify the presence of soft tissue metastasis (Beckett et al., Clin Cancer Res. 1999; 5(12):4034-40). For example, in over half of patients with metastatic disease, diagnosis was made only after radical surgery for the localized tumor (Olsson C A. Urol Clin North Am. 1997; 24(2):367-78). Current research has implied that important diagnostic and prognostic information will be derived only after surgical procedures, where biopsy or radical prostatectomy specimens are surgically removed, and tumor pathology is classified by histological grade and Gleason score. Unfortunately, these invasive methods also have some limitations, such as the need for a highly trained pathologist to interpret the degree of tumor pathology and the histological grade of clinical specimens and the requirement for repeat biopsies in some patients because of missed tumors (Lee et al., Prostate 1999; 39(3):213-8; Noguchi et al. Int J Urol 1999; 6:7-12), and one study reported that up to 26% of men with an initial non-cancer diagnosis were reported positive for prostate cancer on a repeated biopsy performed within one year (O&#39;Dowd et al., Urology. 2000; 55(4):553-9). Patient discomfort and stress is also very high in diagnostic tests based on surgical tissue removal.  
      There is growing evidence that individuals with prostate cancer and other forms of malignant disease exhibit immune responses that can be detected at the level of altered gene expression in leukocytes circulating in peripheral blood. Furthermore, the use of microarray technology allows the simultaneous measurement of the expression levels of up to 14,000 genes transcribed in circulating leukocytes derived from the blood of prostate cancer patients and control individuals. This technology described in this invention demonstrates that individuals suffering from prostate cancer exhibit a conserved pattern, or signature, of gene expression levels in their peripheral blood leukocytes, which is distinct from the corresponding pattern of expression in leukocytes from control subjects. In addition, cpatients with prostate tumors at different histological grades may yield distinct expression signatures that reflect the biological stage and aggressiveness of the tumor, and that information can thus be employed to differentiate among tumors at different pathological stages.  
      This Example demonstrates a novel technique that does not require invasive surgery, yet provides an accurate diagnosis of prostate cancer, and may also provides detailed prognostic information on the stage and biological aggressiveness of the tumor. Investigators have begun to employ microarray technology, based upon sample cDNA probe hybridization to DNA microarrays, to identify and isolate genes differentially expressed in prostate tumor tissues and prostate cancer cell lines. Recent studies have identified genes that may be involved in hormone refractory prostate cancer (Amler et al., Cancer Res. 2000; 60(21):6134-41), and genes that are potential targets for prostate cancer therapy. Many others have applied microarray technology to investigate the LNCaP tumor model cell line series, which re-capitulates some of the major biological stages of prostate tumor progression. These studies have identified genes thought to play a role in the progression of prostate cancer from androgen and bone cell-growth dependence to autonomous metastatic ability (Clelland et al., Am. J. Hum. Genet. 2000; 67:(4) 8).  
      An alternative approach to these experiments has been the development of prostate tissue microarrays, where sectioned tumor tissue is arrayed and immobilized onto the microarray surfaces. Tissue arrays allow more detailed analysis of gene expression within individual prostate tumor cells and has been used to determine and compare profiles of gene expression between tissues of men from ethnic populations that have both low and high risk for developing cancer. Cole et al. (Nat. Genet. 1999: 21(1 Suppl):3841) have proposed the use of tissue microarrays to determine a combined, detailed histological and gene expression 3D reconstruction of the anatomy of normal and prostate malignant tissues, which may ultimately provide vital information in the cellular progression of the disease.  
      Two new studies have been published that are likely to be of great clinical significance for the management of prostate cancer. In one investigation, published in Nature, Dhanasekaran et al., employed normal and neoplastic prostate specimens and cDNA microarrays to analyze and identify gene expression patterns of normal and tumor tissue (Dhanasekaran et al., infra). This study was the first to report specific expression signatures that could distinguish prostate tissue, including normal prostate (adjacent to the tumor site), BPH, localized prostate cancer and metastatic, hormone refractory disease. More recently, a group has employed Affymetrix GeneChip microarrays to analyze prostate tumor specimens and compare gene expression levels among samples of known stages of prostate cancer (Luo et al., Mol Carcinog 2002; 33(1):25-35). Cluster analysis of the measured expression levels identified gene-specific expression patterns from highly aggressive prostate tumors that were distinct from patterns of gene expression in organ confined disease tissue (Luo et al., supra).  
      However, although these investigations of solid tumors provide detailed information on the pathology and malignant process of the tumor, invasive surgery is always necessary to obtain the tumor tissue studied. In contrast, this Example investigates the feasibility of a microarray-based diagnostic test that measures the levels of RNA transcribed from peripheral blood leukocytes of each individual at risk for prostate cancer, and thus does not require surgery to obtain each diagnostic sample.  
      Studies have shown that cancer patients exhibit immune responses that differ from those of control individuals. These studies have also demonstrated that this response can be detected at the level of altered expression of individual genes, e.g., cytokine genes, in leukocytes within peripheral blood. This example employs microarray technology to quantify the gene expression levels of thousands of genes in each prostate cancer patient and control subject&#39;s blood sample, permitting the determination of leukocyte gene expression patterns, or signatures, for each prostate cancer patient and control subject analyzed. Pattern analysis algorithms compare these expression signatures, and define patterns that can distinguish both between normal individuals and those with cancer, and also between patients with prostate tumors at different stages of biological progression. Identification of a leukocyte multigene expression signature specific to prostate cancer, and also characteristic for pathologically defined stages of prostate cancer, provides both diagnostic and prognostic information on individual tumors, and thus play a vital role in prostate cancer pre-biopsy population screens.  
      The results from this experiment form the basis of a pre-biopsy diagnostic screen. A clinical assay initially involves the hybridization of a labeled probe synthesized from RNA extracted from a blood sample drawn from the individual at risk for prostate cancer to a microarray containing a number of genes that are differentially expressed between cancer patients and control individuals. The resultant expression pattern is then compared to a set of known multigene signatures, specific for individual stages of tumor progression for a non-invasive prostate cancer diagnostic assay that can yield both diagnostic and staging information for each individual at risk.  
      Furthermore, since this assay will measure gene expression within leukocytes, instead of circulating malignant cells, and does not rely on the measurement of biomolecules secreted from malignant cells, the resultant assay is sensitive and accurate, and capable of detecting tumors that are still at an early stage of malignancy. Such an assay serves as an important pre-screen that can, with a minimum of patient discomfort, identify men with prostate cancer.  
      Data from investigations of ratios of T cell subsets provides some evidence to correlate serum cytokine levels with mRNA levels (detected by RT-PCR), within peripheral blood from cancer patients. It is therefore likely that the differential prognostic serum levels measured from prostate cancer patient blood will also be detected at the level of mRNA expression. The experimental procedure follows the expression levels of each of the genes mentioned above, and thus determine whether previously reported increases or decreases in serum protein levels in cancer patients correlate with the corresponding mRNA levels detected by microarray analysis.  
      In the work described by Veltri et al., Strom et al., supra and in the other investigations described above, mRNA levels have been quantified individually by RT-PCR techniques. However, this would be extremely time-consuming if many genes were to be analyzed in one experiment. In contrast, this Example employs microarray technology to quantify mRNA transcripts, which allows the simultaneous analysis of thousands of genes expressed in peripheral blood leukocytes. The complex differential gene expression measured using this approach identifies patterns or signatures of gene expression that differ between prostate cancer patients and control subjects, and thus forms the basis of a diagnostic technique.  
      It seems clear that the use of multiple gene products for the determination of expression signatures provides considerably more detailed information on tumor stage and prognosis than can be provided by the quantitation of individual serum protein levels.  
      It should also be noted that although leukocyte gene expression levels will be measured, if, e.g., malignant prostate cells were also present in the blood of patients, then gene expression of these cells will also be quantified. However, it seems likely that the detection of gene expression of malignant cells within blood would actually increase the specificity of this analysis, as mRNA levels arising from circulating metastatic cells would differ from mRNA levels in patients with no metastatic cells in their blood stream.  
     Microarray Technology  
      Oligonucleotide Microarrays. There are two major types of microarray technology; spotted cDNA arrays and manufactured oligonucleotide arrays. The present invention employs high density oligonucleotide Affymetrix® GeneChip arrays (reviewed in Schena at el., Trends Biotechnol. 1999; 16(7):301-6). The Affymetrix system was chosen due to: 1) the large numbers of gene sequences represented within the array, 2) the highly developed Affymetrix protocols for probe preparation and microarray hybridization, and 3) the built-in multiple internal standards. In addition, custom designed normalization software for accurate comparison of results between each individual hybridization accommodates the experimental plan, which involves a direct comparison between individual microarray experiments.  
      A recent investigation of the reproducibility of DNA microarrays has highlighted some problems of reproducibility and comparison among array hybridizations, and the need for replicate experiments. Use of the Affymetrix system eliminates some of the problems that are associated with other microarray technologies, because it provides a significantly lower variation between experiments.  
      Pattern Analysis Algorithms and Computer Analysis. After scanning of each microarray to detect the hybridization signals, Affymetrix® Microarray Suite software is employed for image acquisition and normalization of the fluorescent signals using internal standards. Analysis of the resultant signal intensities over each oligonucleotide, or data point, within each experiment then falls into two main categories: Supervised Learning Algorithms (Golub et al., infra; Slonim et al., 1999; Yeang et al., Bioinformatics. 2001; 17 Suppl 1:S316-22; Ramaswamy et al., infra); and Hierarchical Clustering (Eisen et al., infra; Alizadeh et al., infra; Perou et al., Nature 2000; 406(6797):747-52). All algorithms employed have the capacity to analyze the very large data-sets, and allow comparisons of multiple experiments and multiple points within a single experiment.  
      Affymetrix oligonucleotide microarray technology is employed to simultaneously measure the expression levels of up to about 14,000 genes transcribed in circulating leukocytes derived from the peripheral blood of 40 prostate cancer patients and 20 control individuals. Briefly, leukocytes are extracted from whole blood obtained from prostate cancer patients and healthy controls, and the RNA isolated from these cells is employed to synthesize cDNA, which is then itself employed as a template to synthesize labeled cRNA for hybridization to Affymetrix microarrays. The expression patterns generated for each individual subject sample are compared using data analysis algorithms that have the ability to identify and record multigene expression levels as patterns or multigene signatures.  
      In a specific experiment, leukocytes are collected and subject to sample processing and microarray hybridization. Expression data is derived from microarray hybridization plus data-analysis algorithms to generate multigene expression patterns. The evidence shows that circulating blood leukocytes in individuals suffering from prostate cancer exhibit a characteristic signature of gene expression levels that is different from the signature exhibited by circulating leukocytes from control subjects. Multigene expression signatures in individuals with prostate cancer are specific to the aggressiveness of the tumor from the individual examined, and thus reflect the stage the malignancy has reached in the patient.  
     Materials and Methods  
      Prostate Cancer Subjects. Prostate cancer patients are derived from those undergoing radical prostatectomy (n=50 per year), and those undergoing radiation seed implant therapy (n=150 per year). The total population of prostate cancer patients will be screened for possible recruitment into this study. Informed consent is obtained, according to Institutional Board Regulations. Blood drawing takes place prior to radical surgery or seed implantation.  
      Each patient recruited to participate in this study is provided with a questionnaire designed to obtain both demographic information and information on current general heath. The questionnaire is approved by the Institutional Review Board. Clinical information and pathology reports is also collected for this study. This documentation includes patient history of serum PSA tests, all results of prostatic needle biopsy (Gleason&#39;s stage) and/or clinical and pathological analysis of tumor tissue following surgery (TNM scale, pT stage). CBCs are performed on all recruited patients following blood drawing. Each patient record also has dates of any previous needle biopsy, or other surgical procedures (on average 3-6 months prior to the biopsy).  
      Exclusion Criteria. Patients are excluded if: 1) they have had surgery or other physical trauma less than six weeks prior to blood collection, 2) if they have abnormal CBCs, 3) if they have a current infection, 4) if they have autoimmune disease, 5) if they have had chronic use of immunosuppressants or anti-inflammatory medication. These exclusion criteria have been designed to reduce the likelihood of including prostate cancer patients that exhibit leukocyte gene expression that is different from healthy control subjects, but that arises from factors other than growth and development of a prostate tumor, such as an immune response to surgery or the presence of an infectious agent.  
      Expression signature assays include the screening, recruitment, blood drawing and leukocyte sample preparation of prostate cancer patients. Following removal of red blood cells, the leukocyte cell samples are stable at −70° C. for long periods of time. For each subject, blood will be drawn, processed to isolate leukocyte cells, and then stored at −70° C. Subjects are chosen for complete processing (which involves the extraction of RNA, synthesis of cDNA and cRNA, and microarray hybridization) based on the criteria described below.  
      Microarray analysis measures gene expression levels from 40 of the leukocyte samples collected. The expression data are subjected to supervised learning and clustering algorithms to identify and determine leukocyte gene expression patterns that distinguish between prostate cancer patients and healthy controls.  
      The expression data generated are then used to distinguish among leukocyte gene expression patterns of prostate cancer patients at different diagnosed stages of tumor progression. All patients undergoing treatment, and who are recruited into this study, will have documented reports following needle biopsy (a Gleason score can be documented for each subject). For those patients undergoing radiation seed implantation, further pathological information are not available. Tumors of prostate cancer patients with clinically localized disease can be staged after prostatectomy by the TNM scale (T1, T2 and T3), and also given a more accurate pT stage. The expression data only of men with pathological staging, and thus only of those who will undergo radical surgery are evaluated. Assuming a conservative 20% recruitment of all radical prostatectomy patients (which is below current recruitment levels of prostate cancer subjects), greater than 20 subjects are recruited over the two year period of this proposal.  
      This experiment involves recruitment of subjects, extraction of leukocytes and completed sample processing for every prostate cancer patient who satisfies the following criteria: undergoes radical prostatectomy or radiation seed implantation, consents to take part in this proposal, does not fall within the exclusion criteria, and has detailed tumor stage information available.  
      Control Subjects. Twenty control male subjects, approximately age-matched to prostate cancer patients, are recruited from the staff and staff relatives. Informed consent is obtained, according to Institutional Board Regulations. Each control subject recruited to participate in this study is provided with a questionnaire to obtain both demographic information and information on current general heath. The questionnaire is approved by the Institutional Review Board. Information collected through the completion of this questionnaire is employed as described above, as well as to determine that a control subject is unlikely to have an undiagnosed prostate tumor, or other solid tumor, that may effect leukocyte gene expression. Blood samples are drawn by a trained phlebotomist from the antecubital vein using a needle and evacuated tube. For each control subject chosen to take part in this study, serum PSA levels are measured, and CBC counts performed.  
      Exclusion criteria for controls. Control subjects are excluded from this study if: 1) they have serum PSA levels &gt;4 ng/ml, 2) if they have abnormal CBCs, 3) if they have experienced discomfort while urinating, 4) if they have a first-degree relative diagnosed with prostate cancer or any other solid tumor, 5) if they have documented a current infection, 6) if they have autoimmune disease, 7) if they have had surgery or other physical trauma less than six weeks prior to blood collection, 8) if they have had chronic use of immunosuppressants or anti-inflammatory medication.  
      Potential Problems Arising from Factors Other than Prostate Cancer. During recruitment of both prostate cancer patients and control subjects, it is clear that attention must be paid to the possibility that the mRNA levels of some of the genes expressed in leukocytes, in both patients and control subjects, may change because of underlying inflammatory disease states or other illness. As described above, both prostate cancer patients and control subjects are otherwise normal healthy individuals with no history of autoimmune disease or current infection. It is unlikely that any control subject has an undiagnosed prostate or other solid tumor.  
      However, it is well known that individuals possess different immune complements, and these may well be detected within individual experiments. Flagging is a method employed to normalize between patient samples and thus will be employed to reduce some of the inter-subject variability that may be detected following microarray hybridization. Any gene found to be significantly differentially expressed (&gt;3 fold change) between two or more of the normal control individuals, will be “flagged”, which subsequently removes this gene from any further analysis. This method was successfully used to remove inter-subject variation from both multiple patient samples such as total lymph nodes, and also from multiple cell lines of different lineages that were employed to identify profiles of gene expression in B cell lymphomas (Alizadeh et al., supra).  
      It should be noted that the algorithms described in detail below have been successfully employed to identify gene expression profiles that distinguish complex tumor tissue from normal non-disease tissue (that has not undergone micro-dissection procedures), and thus are not hindered by complex patterns of total gene expression.  
      Use of the Affymetrix Oligonucleotide Microarray Technology. The Affymetrix system appears to be better suited to the present project than a cDNA microarray-based system. Therefore, Affymetrix Human Genome U133A oligonucleotide microarrays are employed to analyze gene expression signatures in peripheral blood leukocytes taken from the prostate cancer patients described above, and in corresponding cells from control subjects recruited during this study. This array is an upgraded version of the HU95A arrays employed in the preliminary studies, and will soon replace this array. The arrays are comparable with each other.  
      Affymetrix Human U133A oligonucleotide microarrays contain about 14,000 individual human sequence verified oligonucleotides, representing Unigene, GenBank and TIGR database clusters that have been previously characterized by function and disease association. The specific gene products described above are all represented on this microarray and thus are included in all analytical procedures. Furthermore, many other genes known to be involved in immune responses are also included on this microarray, such as multiple cytokines and growth factors, e.g., osteopontin, which has been found to be up-regulated in prostate tumor models (Thalmann et al., Cancer Res. 1999; 54(10):2577-81), and shown functionally to play a role in cell mediated immunity.  
      Sample Processing, Probe Preparation and Microarray Hybridization. All blood samples are processed immediately following collection; leukocytes are extracted from blood using lysis buffers and centrifugation, according to standard procedures. The leukocytes are stable at −70° C. for long periods of time (&gt;6 months, Qiagen). The storage of leukocytes at that temperature allows the retrospective determination of which samples are to be hybridized to GeneChips, after a detailed analysis of all available patient history and a confirmed histological analysis of biopsy samples and prostate tissue in the case of patients undergoing surgery. All patient and control samples chosen for RNA extraction are processed in duplicate, by splitting the white blood cell sample extracted from whole blood and processing the duplicate samples identically thereafter. The need for replicate microarray experiments has been previously highlighted, so each sample is processed in duplicate. This experimental design was based on the reproducibility of Affymetrix arrays, hybridization protocols and scanning (mean R2=0.98 and 0.967 for repeat hybridization, and duplicate sample processing respectively), and previously reported use of duplicate hybridizations in microarray experiments (Chen et al., J Cell Biol 2000; 151:1321-36).  
      Data Analysis. Following image acquisition and normalization using Affymetrix software and protocols, the data analysis employs two major algorithm types; Hierarchical Clustering (Eisen et al., infra; Alizadeh et al., infra; Perou et al., infra) and Supervised Learning Algorithms; Group Classification (Golub et al., supra; Slonim et al., infra), and Support Vector Machine (Yeang et al., supra; Ramaswamy et al., infra). Use of each of these techniques is described in detail below.  
      Hierarchical Clustering. Leukocyte expression signatures discriminate between cancer patients and control, matched subjects, and also to attempt to distinguish among individual stages of the prostate tumors analyzed. Data analysis initially employs a hierarchical clustering algorithm that has been successfully applied to classify gene expression data in several studies of human tumors, and is briefly described as follows. The Cluster program (M. Eisen), employs a fast two-way clustering that is based upon a similarity metric between genes and experimental samples. A standard Pearson correlation coefficient is employed to perform multiple iterations of similarity measurements between each data point (microarray probeset intensity value) within the vertical axis, thus expression levels between every gene in the data-set. Relationships among genes are represented by a tree, whose branch distance lengths reflect the degree of similarity between genes. This distance can be calculated depending on the amount of constraint needed; as a single-linkage cluster (where Cluster calculates the minimal distance between two genes), an average-linkage (calculates the average distance), or complete-linkage cluster which is the most conservative measurement of gene expression similarity that calculations the maximum distance.  
      The clustering procedures yield a binary tree where genes are near each other on the tree if they are strongly correlated, and branches of similarly expressed genes group into discrete nodes. The same algorithm is then applied to cluster the experimental samples according to their overall patterns of gene expression.  
      A graphic display of the intensities of the genes by individual subjects is then created in the program TreeView (M. Eisen). Intensity of each gene is normalized by median centering and represented by a color scheme varying from red for high intensities to green for low. The genes are ordered along the vertical axis using the binary tree from the first cluster analysis. The subjects are arranged across the horizontal axis according to the second binary tree. This visual representation of the data shows clusters of genes that exhibit similar expression intensity among each individual subject.  
      Hierarchical clustering is performed on all 40 prostate cancer patients and 20 control subjects recruited during this study. The gene expression data will correctly classify patients from controls. It should be noted that the hierarchical Clustering algorithm will cluster only those genes that exhibit a similar pattern of leukocyte expression among subjects. Thus, differential gene expression that arose, e.g., from an irregular immune response in only one individual will not be included in the cluster of similarly expressed genes among all subjects. Although this may result in some genes being removed from analysis due to variable levels in some subjects, this algorithm will act to reduce the influence of the many non-PCa related gene expression changes that may be detected when analyzing so many data points.  
      Expression profiles can distinguish prostate tumor samples according to the stage of tumor aggressiveness. The results derived from the clustering algorithms should correlate with tumor stage, e.g., all patients with a defined stage of T3 should cluster together in a sub-node, away from sub-nodes of different staged tumors. To analyze Cluster results all TreeView readout data are compared with the detailed surgical report pathology provided for each patient employed in this analysis to identify clusters of patient samples that fall within similar clinical and pathological tumor stages. Such an approach has been successfully applied to distinguish among populations of both B-cell lymphomas (Alizadeh et al., supra), multiple breast tumors (Perou et al., 2000) and prostate tumor tissue (Dhanasekaran et al., supra).  
      It may prove useful to perform a supervised clustering experiment, as this Example employs a surrogate tissue in which differences in the patterns of gene expression of leukocytes from tumor patients may be more subtle than the differences obtained from analysis of the tumor tissue itself. Supervised clustering can be performed using adjustments within the Cluster program. For example, for the initial data analysis each sample was given equal weighting i.e., each sample was assigned equal importance (and thus defined as unsupervised). If the weighting of the samples is altered and the data is then analyzed in Cluster using GORDER, which provides a constraint on the algorithm to keep the samples in particular groups (e.g., groups of prostate cancer patients at disease T2 versus groups of patient at T3), the horizontal axis of gene similarities will be defined by this order. In this instance, branch length within and between nodes can be employed to identify genes with similar expression patterns between the selected groups.  
      Finally, genes that are significantly differentially expressed between subgroups of patients and/or subgroups of controls (that have not been removed by flagging procedures) may have strong weighting on the final clustering results. This may alter the final nodes of the clusters and even skew the overall cluster data. Therefore statistical tests, such as the student T-or Wilcoxin test (ensuring that in each instance there are sufficient sample numbers for analysis), are performed to identify, and then remove from analysis, genes significantly differentially expressed between, all control subjects. This procedure should help to greatly reduce the inter-subject variation.  
      Supervised Learning Algorithms. Supervised learning algorithms are based on an initial definition of the subject groups to be distinguished by the algorithm. A sub-set of each group is employed to determine characteristics that can separate the two groups, in this case gene expression levels. The characters, or genes, that play a role in the separation, are then used on a test set of data (the remaining subjects), to call each test sample. Two algorithms employed for this analysis are briefly described below.  
      Group Classification. Group Classification (Golub et al., 1999; Slonim et al., 1999), has been recently used to investigate genetic differences between leukemia&#39;s, elucidating gene expression distinctions between two forms of this disease. This algorithm will be used to evaluate and compare the results generated through the hierarchical clustering method. Following procedures employed by Golub et al., (supra) subjects are divided into two sets: the “training set” includes 20 prostate cancer patients and 10 normal control subjects; the “test set” includes an additional 20 tumor patients and 10 control subjects. A multigene expression signature is constructed using the 30 subjects from the “training set”, as follows. First, all genes are sorted by the degree of correlation between the expression level and subject diagnosis, in this case being positive or negative for prostate cancer. A correlation metric which measures relative class separation is used [correlation metric P(g,c)=(μ1−μ2)/(σ1+σ2) where g=the expression vector of a gene over n samples and c=the diagnostic class vector]. The significance levels of these correlations is then determined using a permutation test called “neighborhood analysis” Taking the significantly correlated genes, different subsets of genes are then tested to find the best model for classifying diagnosis using cross validation procedures within the “training set”.  
      The final model is then used with the “test set” of additional patients and controls, to see if subjects can be correctly classified with a positive or negative tumor diagnosis. Each gene “votes” for cancer or normal diagnosis, based on whether its expression level is closer to the mean expression level of prostate cancer patients or of normal controls. This vote is weighted by the degree of correlation between the gene and diagnostic group. Votes across all genes are summed to make a final classification of diagnosis, provided there is sufficient prediction strength as measured by the margin of “victory” [prediction strength=(V winner −V loser )/(V winner +V loser ) where V is then number of “Votes” received for each diagnosis]. Classification of subjects is evaluated in terms of error rate (% incorrect classifications) and “no-call” rate (% of samples considered “uncertain”).  
      Support Vector Machine. A support vector machine (SVM) supervised learning algorithm has recently been employed to perform multiclass cancer diagnosis of 14 different tumor classes and control tissues, and is employed for analysis of the prostate and control sample leukocyte gene expression data. Data input for this algorithm is similar to group classification, whereby subjects are divided into training and test sets. The training set is then characterized by labeling or classing each subject as positive +1 (e.g., prostate cancer samples) or negative −1 (e.g., control samples). SVM finds a hyperplane, w, which separates positive and negative training samples and maximizes the margin, or distance, between the samples and the hyperplane, where f(x)=w·x+b. The geometric property can be imposed by means of the following optimization problem: minimize½∥w 2 ∥ subject to y i (w·x i +b)≧1, for all i (where x is the input data, e.g. expression level; y is the class label +1 or −1). The discriminate function can be written as f(x)=Σw i y i (x·x i )+b, where w i &#39;s and b can be obtained from solving the quadratic function. The hyperplane is then employed for classification of the test set, where an unknown test samples position relevant to the hyperplane determines its class, and the confidence of each SVM prediction is based on (and is proportional to), the distance of the test sample from the hyperplane.  
      The SVM described above results in a binary classification, which is employed to distinguish between the two groups of 40 prostate cancer patients and 20 control subjects. Evaluation of the ability of the algorithm to correctly group patients and controls will determine which genes are major effectors in the classification, and the statistical power of each for each sample.  
      In the papers referenced above, a one-versus-all (OVA) approach has also been employed to perform multiclass prediction. The OVA builds k (the number of classes) binary classifiers which distinguish one class from all the other lumped together (Yeang et al., 2001; Ramaswamy et al., 2001). For a test sample x, the binary classifier outputs form a k-vector f(x)=(f i (x), . . . ,f k (x)). If f (x) is a real number (i.e., a predicted class with confidence value), then the predictor finds the maximum of f i (x) and assigns the sample to the corresponding class label. Using this approach, Ramaswamy et al., created a multiclass cancer gene expression database from 144 human cancers and normal tissues from a total of 14 classes, and demonstrated a 78% accurate classification/diagnosis of the correct cancer or control tissue over the set of test samples (n=54) (Ramaswamy et al., supra). An OVA approach, where k=each stage of prostate tumor (i.e., T1-3(4)) can be employed here.  
     Analysis of Leukocyte Gene Expression and The Multigene Expression Signatures Determined Following Data Analysis  
      Quantitative RT-PCR. Although recent reports have documented the reliability and reproducibility of microarray analysis, this powerful technology is still in its infancy and it may be necessary to perform additional confirmation of the expression results obtained. Therefore, gene specific primers are designed for a number of genes seen to be differentially regulated among leukocytes obtained from cancer patients and controls, and employed for assay via real-time RT-PCR of leukocyte transcript levels. The actual number of genes employed for validation of results depends on the number of genes found in this assay to be differentially expressed. Microarray experiments performed by other researchers, and cited above, are available as guidelines for this analysis. Genes chosen for this analysis include those identified in previous studies that are differentially regulated between leukocytes from patients with a solid tumor relative to leukocytes from control subjects (and are thus positive controls), and also genes included in the multigene signatures deduced through the data analysis. For each gene analyzed, RT-PCR analysis is used confirm and validate the outcome of the microarray analysis.  
     Example 4  
     Breast Cancer Diagnosis Bloodcell Multigene Signatures  
     Introduction  
      Breast cancer is the second leading cause of cancer deaths in North American women. It has been estimated that in 2002, 203,500 new cases of breast cancer were diagnosed in the US, with approximately 39,600 deaths in that year alone (Jemal et al., 2002) Current techniques for the screening of breast cancer, as a prerequisite to biopsy for diagnostic evaluation of the detected mass, include physical breast examination and mammography. These techniques possess a number of limitations, including lack of specificity and accuracy in the diagnosis and, also a lack of cancer stage and prognostic information. This ultimately yields high numbers of false positive diagnoses, and consequently unnecessarily large numbers of surgical biopsies. The rationale behind this proposal is based on two sources of data: 1) Current scientific literature, in which there is growing evidence that individuals with breast cancer and other forms of malignant disease such as prostate cancer, exhibit immune responses that can be detected at the level of altered gene expression in leukocytes circulating in peripheral blood. Quantitation of the mRNA transcripts in leukocytes of a number of individual genes has demonstrated associations between gene expression levels and the presence of a tumor in patients with breast and prostate cancer. 2) Preliminary results from a microarray study investigating gene expression changes in men with prostate cancer. Initial results from this study have been striking; supervised cluster analysis of peripheral leukocyte gene expression data, using transcript level measurements of thousands of genes from eleven prostate cancer patients and seven matched control subjects, resulted in a classification of all the subjects into their correct group.  
      The use of microarray technology allows the simultaneous measurement of the expression levels of up to 14,000 genes transcribed in circulating leukocytes derived from the blood of breast cancer patients and control individuals. This technology, demonstrates that women suffering from breast cancer exhibit a conserved pattern, or signature, of gene expression levels in their peripheral blood leukocytes, which is distinct from the corresponding pattern of expression in leukocytes from control subjects. Patients with breast cancers at different histological grades, yield distinct expression signatures that reflect the biological stage and aggressiveness of the cancer, and that information can thus be employed to differentiate among breast cancers at different pathological stages.  
      This Example demonstrates a novel technique that does not require invasive techniques to obtain tumor tissue, yet provides an accurate diagnosis of breast cancer, and also provides detailed prognostic information on the stage and biological aggressiveness of the tumor. The success of this project would yield a much needed, non-invasive tool for stage-specific diagnosis of the disease, and thus serve as an important screening tool to identify women with breast cancer.  
      Although mortality rates have decreased over the past decade, through pre-symptomatic screening programs and major improvement in breast cancer treatment, breast cancer survival rates decrease dramatically in women with a more advanced stage at diagnosis and it has been estimated that only half of all breast cancers are localized at the time of diagnosis. Thus, effective management of breast cancer relies heavily on an early diagnosis, coupled with a need to obtain accurate information on the classification and stage of the cancer itself, and thus limitations of traditional diagnostic and prognostic techniques may currently hinder the management of breast cancer.  
      Although frequently advocated, evidence to support the use of breast self examinations (BSE) in screening programs is weak. To date, no study has evaluated the effectiveness of clinical breast examinations (CBE) as a stand-alone screening technique. Widespread adoption of screening mammography, which utilizes ionizing radiation to image breast tissue, has been accredited with the dramatic increase in incidence rates of breast cancer between 1980-1987, illustrating the benefit of screening programs in identifying the presence of breast cancer. However, there has been much recent controversy over the benefits versus the risks of regular mammography (reviewed in Humphrey et al., supra). Thus, in large mammography screening programs, for every one hundred dollars spent on screening thirty three will have been spent on the evaluation of false positive results (Elmore et al., N Engl J Med. 1998; 338(16):1089-96).  
      Other techniques include the use of ultrasound in the evaluation of palpable or mammographically identified masses, and the use of serum tumor markers for the detection of breast cancer, such as CA15.3, lack sensitivity and specificity (Chan D. W., 2001) and research has focused on the use of PCR-based approaches for tumor micrometastasis detection. Quantitative RT-PCR analysis of gene products, in malignant cells that have survived detachment from the original tumor site and circulation within peripheral blood, has been employed to identify metastatic disease, and detection of circulating levels of the mRNAs transcribed by the genes CK-19, MUC1, CEA and mammoglobin, has been reported to provide both diagnostic and prognostic information on breast cancer (Berois et al., Eur J Cancer 2000; 36(6):717-23). However, problems with these methods have been documented such as the detection of CK-19 pseudogenes that can contaminate results, and the lack of replication and lack of tissue specific expression detected following analysis of mammoglobin.  
      Research has implied that some important diagnostic and prognostic information will be derived only after surgical procedures, and in current clinical practice an actual diagnosis of breast cancer is made following pathologic review of a tissue specimen. Breast tissue can be obtained by the methods of excisional or incisional biopsy, where the entire palpable mass or a section of the mass (respectively) is surgically removed. Although accurate, these techniques are very painful for the patients and lead to extensive scarring (which can mimic a malignancy on physical or mammographic examination).  
      Differential Expression Of Individual Genes In Leukocytes From Patients With Breast Cancer. The tumor derived antigen 90K (Mc-2 BP) is a widely expressed, secreted glycoprotein found in the serum of healthy individuals. Levels of the 90k protein are significantly increased in the serum of patients with breast cancer, and Fusco et al., showed that 90K serum protein levels were also elevated in 20% of patients with no clinical evidence of the disease (et al., Int J Cancer. 1998; 79(1):236). Fusco et al., additionally showed that transcript levels of the 90K gene were also higher in patients versus controls, and they suggest that peripheral blood cell monocytes (isolated from whole blood) may be activated in response to breast cancer growth and progression.  
      Martin et al., performed an targeted microarray based investigation using RNA template derived from blood of breast cancer patients (DCIS to Stage IV), (et al., Proc Natl Acad Sci USA.; 98(5):2646-51). Genes were chosen to be placed on the array if they were found to be differentially expressed between breast cancer tissue and control breast tissue by differential display (n=170). Cluster analysis identified a group of 12 genes that were elevated in 77% of the subjects with more aggressive cancer, including the genes maspin, CD44 and HER2. However, although the authors hypothesize that they are detecting disseminated breast cancer cells (Martin et al., supra), they suggest that their results may also arise from the detection of mRNA transcripts within the leukocytes themselves. Evidence to support this alternate hypothesis also comes from preliminary studies measured leukocyte expression levels were measured in prostate cancer patients and control subjects. The genes maspin, CD44 and HER2 were all found to be significantly expressed above background levels in all subjects, and HER2 was shown to be up-regulated in prostate cancer patients. As described above, experiments that show the accurate classification of prostate cancer subject and healthy control subjects into their respective groups, based on the expression levels of over 1500 gene, provide evidence to support breast cancer diagnosis though leukocyte expression signatures. The genes employed above for classification of prostate cancer will not necessarily be the exact genes employed for classification of breast cancer. However, extensive literature has been published documenting the common similarities between breast and prostate cancer, including incidence and mortality rates, risk factors, initiation of transformation, and roles of androgens and estrogens (reviewed in Lopez-Otin &amp; Diamandis Endocr Rev.; 19(4):365-96). These data, along with results presented infra, provide evidence that growth and development of a breast cancer will exert an effect on the immune system that can be detected at the level of altered gene expression in peripheral blood leukocytes.  
      This Example employs microarray technology to quantify mRNA transcripts, which allows the simultaneous analysis of thousands of genes expressed in peripheral blood leukocytes. The complex differential gene expression measured using this approach identifies patterns or signatures of gene expression that differ between breast cancer patients and control subjects, and thus forms the basis of a diagnostic technique.  
      It seems clear that the use of multiple gene products for the determination of expression signatures provides considerably more detailed information on tumor stage and prognosis than can be provided by the quantitation of individual serum protein levels. It should also be noted that although leukocyte gene expression levels will be measured, if, e.g., malignant breast cells were also present in the blood of patients, then gene expression of these cells will also be quantified. It seems likely that the detection of gene expression in malignant cells within blood would actually increase the specificity of this analysis, as mRNA levels arising from circulating metastatic cells would differ from mRNA levels in patients with no metastatic cells in their blood stream.  
      Affymetrix oligonucleotide microarray technology is employed to simultaneously measure the expression levels of up to about 14,000 genes transcribed in circulating leukocytes derived from the peripheral blood of 55 breast cancer patients and 25 control individuals as described above. In a specific experiment, leukocytes are collected and subjected to sample processing and microarray hybridization. Expression data derived from microarray hybridization plus data-analysis algorithms to generate multigene expression patterns is used for analysis. These data show that circulating blood leukocytes in individuals suffering from breast cancer exhibit a characteristic signature of gene expression levels that is different from the signature exhibited by circulating leukocytes from control subjects. Multigene expression signatures in individuals with breast cancer are specific to the aggressiveness of the tumor from the individual examined, and thus reflect the stage the malignancy has reached in the patient.  
     Materials And Methods  
      Breast cancer subjects. The experimental approach measures leukocyte gene expression levels in 55 breast cancer patients, and 25 matched control subjects, with duplicate sample processing of each subject. Duplicate processing was performed to permit the robustness of a cancer-specific gene expression signature to be determined. The microarray technology and pattern analysis algorithms and analysis are the same as for the prostate study in Example 3.  
      All breast cancer patients are potential candidates for enrollment into this study, and this total population of breast cancer patients is screened for possible recruitment into this study. Informed consent is obtained, according to Institutional Board Regulations. Blood drawing takes place following initial diagnosis or confirmation of breast cancer diagnosis, and prior to the onset of treatment for the disease. Treatment options for breast cancer are generally directed by the stage that the tumor has reached in that individual. For example, treatment for Stages I and II most often involves a combination of surgery and radiation therapy and/or adjunct systemic therapy. Treatment for stage III, which is characterized by lymph node involvement, may alternatively start with chemotherapy, followed by surgery and radiation therapy. Patients from stages I, and II, and stage III will be included only if recruitment and blood drawing was performed prior to the initiation of therapy. Additionally, patients with advanced metastatic disease may also be recruited if they are screened for participation prior to the onset of treatment for localized and metastatic disease.  
      Annual estimates of patients available at stages I, II, and III are about 80-100. It is not contemplated to specifically screen and exclude patients based on actual tumor stage, or the presence of metastatic disease. This broad inclusion should allow recruitment of at least 20 patients from stages I-III.  
      Each patient recruited to participate in this study is provided with a questionnaire designed to obtain both demographic information and information on current general heath. The questionnaire is approved by the Institutional Review Board. Clinical information, biopsy reports (including dates of biopsy), and any further pathology reports are also collected for this study. This documentation includes all patient history, all results of any mammography, ultrasound, and core needle biopsy. CBCs is performed on all recruited patients following blood drawing.  
      Exclusion Criteria for Patients. Patients will be excluded from this study if: 1) they have had surgery or other physical trauma less than six weeks prior to blood collection, 2) if they have abnormal CBCs, 3) if they have a current infection, 4) if they have autoimmune disease, 5) if they have had chronic use of immunosuppressants or anti-inflammatory medication. These exclusion criteria have been designed to reduce the likelihood of including breast cancer patients that exhibit leukocyte gene expression that is different from healthy control subjects, but that arises from factors other than growth and development of a breast cancer, such as an immune response to surgery or the presence of an infectious agent.  
      Control subjects. Twenty-five control female subjects, approximately age-matched to breast cancer patients, are recruited from the staff and staff relatives. Informed consent is obtained, according to IRB regulations. Each control subject recruited to participate in this study is provided with a questionnaire to obtain both demographic information and information on current general heath. The questionnaire is approved by the Institutional Review Board. Information collected through the completion of this questionnaire is employed as described, as well as to determine that a control subject is unlikely to have an undiagnosed breast, or other solid tumor, that may effect leukocyte gene expression. Blood samples are drawn by a trained phlebotomist from the antecubital vein using a needle and evacuated tube. For each control subject chosen to take part in this study, CBC counts are performed. Clinical Breast Examinations for control subjects are also performed. Control subjects are informed, in writing, of the results of their CBE.  
      Exclusion Criteria for Controls. Control subjects are excluded from this study if: 1) they have abnormal CBCs, 2) they have a high risk factor for developing breast cancer, such as two first-degree relatives with the disease, 3) if they have a first-degree relative diagnosed any other solid tumor, 4) if they have documented a current infection, 5) if they have autoimmune disease, 6) if they have had surgery or other physical trauma less than six weeks prior to blood collection, 7) if they have had chronic use of immunosuppressants or anti-inflammatory medication. Control subjects are excluded if a palpable mass is detected by CBE.  
      Potential Problems Arising from Factors Other Titan Breast Cancer. During recruitment of both breast cancer patients and control subjects, it is clear that attention must be paid to the possibility that the mRNA levels of some of the genes expressed in leukocytes, in both patients and control subjects, may change because of underlying inflammatory disease states or other illness. As described above, both breast cancer patients and control subjects are otherwise normal healthy individuals with no history of autoimmune disease or current infection. It is unlikely that any control subject has an undiagnosed breast carcinoma or other solid tumor.  
      However, it is well known that individuals possess different immune complements, and these may well be detected within these experiments. Flagging is a method employed to normalize between patient samples and this will be employed to reduce some of the inter-subject variability that may be detected following microarray hybridization. Any gene found to be significantly differentially expressed (&gt;3 fold change) between two or more of the normal control individuals, will be “flagged”, which subsequently removes this gene from any further analysis. This method was successfully used to remove inter-subject variation from both multiple patient samples such as total lymph nodes, and also from multiple cell lines of different lineages that were employed to identify profiles of gene expression in B cell lymphomas (Alizadeh et al., Nature 2000; 403(6769):503-11). It should be noted that however that this approach to remove gene expression variability, or “noise”, was not employed in the preliminary studies, as supervised hierarchical clustering analysis was performed, where expression noise can be removed from the data set prior to input into the data analysis algorithms. Furthermore, flagging genes may eliminate too many genes from analysis. With this in mind, expression analysis is performed on the data sets pre- and post-flagging.  
      The algorithms described in detail below have been successfully employed to identify gene expression profiles that distinguish complex tumor tissue from normal non-disease tissue (that has not undergone micro-dissection procedures), and thus are not hindered by complex patterns of total gene expression.  
      Use of the Affymetrix Oligonucleotide Microarray Technology. The Affymetrix system appears to be better suited to the present project than a cDNA microarray-based system. Therefore, Affymetrix Human Genome U133A oligonucleotide microarrays are employed to analyze gene expression signatures in peripheral blood leukocytes taken from the breast cancer patients described above, and in corresponding cells from control subjects recruited during this study. This array is an upgraded version of the HU95A arrays employed in the preliminary studies, and will soon replace this array. The arrays are comparable with each other.  
      Affymetrix Human U133A oligonucleotide microarrays contain about 14,000 individual human sequence verified oligonucleotides, representing Unigene, GenBank and TIGR database clusters that have been previously characterized by function and disease association. The specific gene products described above are all represented on this microarray and thus are included in all analytical procedures. Furthermore, many other genes known to be involved in immune responses are also included on this microarray, such as multiple cytokines and growth factors, and e.g. maspin, which has been found to be down-regulated in breast cancer mouse models.  
      Sample Processing, Probe Preparation and Microarray Hybridization. All blood samples are processed immediately following collection; leukocytes are extracted from blood using lysis buffers and centrifugation, according to standard procedures. The storage of leukocytes at that temperature allows the retrospective determination of which samples are to be hybridized to GeneChips, after a detailed analysis of all available patient history and a confirmed histological analysis of biopsy samples (and tissue, in the case of patients undergoing surgery after their participation in this study). All patient and control samples chosen for RNA extraction are then processed in duplicate, by splitting the white blood cell sample extracted from whole blood and processing the duplicate samples identically thereafter.  
      Replicate Sample Processing Versus Non-Replicates. The need for replicate microarray experiments has been previously highlighted (Lee et al., 2000). There is much discussion in the scientific community on the need for replication, and biostatisticians have suggested that a lack of replication will restrict the use of formal statistical tests. Sources of variation and necessary levels of replication vary considerably among the array platforms to be employed, however Dudoit et al., have suggested that many considerations on replication are applicable to both cDNA and oligonucleotide platforms (Statist. Sincia. 2000; 12, 111-139).  
      The term biological replication can have two meanings; “actual biological replication” is the replication of array processing and hybridization involving mRNA from different extractions from the same sample or individual, and “biological replication”, where target mRNA comes from, e.g., different version of a cell line, or different individuals. These forms of replication are very different in nature, with the latter involving a much greater degree of variation in measurements (Yang et al., Nat Rev Genet. 2002; 3(8):579-88). For the efficient design of this study the choice of biological replication is very important. For example, it may be that variation between individuals will be larger than other sources of variation (i.e. experimental), and thus it may be inefficient to perform replicate arrays from a small number of samples. However, Simon et al., Genet Epidemiol. 2002; 23(1):21-36, have suggested several motivations for performing actual biological replication, as this replication provides an estimation of the reproducibility of the experimental procedures, it permits the identification and discarding of “bad” arrays, and actual biological replication can improve precision of the estimate of the expression profile for a given RNA sample though the averaging of multiple arrays. Furthermore, replicate samples are extremely useful when attempting to establish that a classification between diseases is robust, which is particularly true for class discovery algorithms, where the large number of genes make it relatively easy to discover interesting patterns of gene expression, even in random datasets.  
      The Affymetrix system provides a significantly lower variation between experiments, suggesting that the need for 3 or more replicates can be reduced. Additionally, each sample is processed in duplicate, thus performing actual biological replications. The above considerations, in particular that the robustness of the classification is deemed essential, coupled with the frequently reported use of duplicate hybridizations in Affymetrix oligonucleotide array experiments, and the use of actual biological replicates in two landmark papers on identification of breast cancer expression profiles (Perou et al., Nature 2000; 406(6797):747-52; Van t&#39;Veer et al., Nature 2002; 415(6871):530-6) justifies the use of duplicate sample processing.  
      Data Analysis. All data analysis is performed as described for prostate cancer expression profiling in Example 3.  
     Analysis of Leukocyte Gene Expression and the Multigene Expression Signatures Determined Following Data Analysis  
      Quantitative RT-PCR to Confirm the Results of the Microarray Experiments. For validation of microarray results, primers are designed to amplify a number of genes seen to be differentially regulated among leukocytes obtained from breast cancer patients and controls, and employed for assay via real-time RT-PCR of leukocyte transcript levels. The actual number of genes employed for validation of results depends on the number of genes found to be differentially expressed. Microarray experiments performed by other researchers, and cited above, are available as guidelines in determining the number of gene that need to be analyzed to validate the microarray results. Genes chosen for this analysis include those identified in previous studies that are differentially regulated between leukocytes from patients with a solid tumor relative to leukocytes from control subjects (and are thus positive controls), and also genes included in the multigene signatures deduced through the data analysis. For each gene analyzed, RT-PCR analysis is used to confirm and validate the outcome of the microarray analysis.  
     Example 5  
     Psychiatric Illness with Multigene Expression Classification  
     Introduction  
      Previous studies have shown associations between white blood cell (leukocyte) gene expression levels and the psychiatric disorders bipolar disorder (BPD) and schizophrenia (SZ). As shown in the Example above, patients with SZ have a characteristic leukocyte multigene expression pattern or signature that differs from healthy control subjects. The positive expression data results collected for schizophrenics (n=8) and healthy controls (n=5), in addition to the contrasting gene expression differences reported between healthy controls, and patients with BPD or SZ [Spleiss et al., Mol Psychiatry 1998; 3, 512-20; Ilani et al., Proc Natl Acad Sci USA 2001; 98(2), 625-628)], establishes that specific leukocyte multigene expression profiles can differentially classify psychiatric illness.  
      This Example generates gene expression data from patients with BPD and SZ. The data create classifying multigene expression profiles for each of the disorders, using hierarchical clustering and supervised learning algorithms, that can be used to correctly distinguish leukocyte samples taken from patients with either BPD or SZ. This in turn leads to improved treatment targeting for patients with BPD and SZ, following classification with multigene expression profiles. This work also establishes the ability to define those at risk for the development of BPD and SZ based on the multigene expression signatures.  
     Rationale  
      The psychiatric disorders to be investigated during this proposed study, BPD and SZ, have incidences in the general population of approximately 1%. Susceptibility to these disorders includes a large but variable genetic component, and there are efforts currently underway to find genes that play roles in the development of the diseases, through linkage analysis and association studies. Several chromosome regions and genes have been suggested as candidates for disease loci (Tsai et al., J Affect Disord 2001; 64, 185-93; Cloninger et al., Am. J. Med. Genet. 1998; 81, 275-281). Physical, biological and environmental factors such as birth trauma low birth weight, poor fetal nutrition, viral infection, autoimmune processes and winter/spring birth are also thought to contribute to the risk of developing BPD and SZ, as they may impact the developing brain either in utero or during postnatal development Kinney et al., J Affect Disord 1998; 50, 117-24; Gunduz et al., Schizophr Res. 1999; 40, 237-433). There are currently no genetic or biochemical markers or tests which can specifically predict the onset of these psychiatric illnesses or differentiate between the disorders.  
      A biological assay providing information that could help classify BPD and SZ, and define susceptibility at an early stage, especially in high risk families, may allow targeted treatment strategies to commence before the onset of many symptoms.  
      There is a growing literature illustrating the usefulness of global gene expression measurements in the characterization and classification of diseases and their subtypes, such as prediction of patient survival time, and response and sensitivity to treatment (see e.g., Sorlie et al., Proc Natl Acad Sci USA 2001; 98, 10869-74 In parallel to the above Examples, and of interest to this Example, Hoffman et al. recently described the first disease classification, by microarray analysis of brain tissue, between Rett syndrome patients and controls (Colantuoni et al., Neurobiol Dis. 2001; 8, 847-65).  
      To date, published microarray analyses of samples from patients with SZ and BPD have focused on analysis of post mortem brain tissue to investigate their etiologies. Upon microarray analysis of prefontal cortex, one group has suggested SZ is a disease of the synapse, and that expression analysis of genes involved in the regulation of presynaptic function may elucidate different sub-types or etiologies of SZ (Mirnics et al., Trends Neurosci, 2001; 24, 479-86). The results of a study employing Affymetrix GeneChips showed altered expression of genes involved in different functions, such as myelination, again providing detailed data on biological processes in the brain of SZ patients.  
      Although microarray analysis of brain samples has, and will provide important information on the etiology and pathogenesis of BPD and SZ, it is obvious that use of brain samples from living patients for molecular diagnostic classification is not feasible. Thus, the development of any multigene expression-based classification of BPD and SZ should focus on a tissue that is accessible. Peripheral blood samples are easily obtained and most significantly, it has previously been reported that SZ and BPD patients have altered levels of multiple gene products that are expressed in blood leukocytes. In a recent report, Ilani et al. measured the mRNA levels of the Dopamine D3 receptor gene in leukocytes from SZ patients and matched control subjects. They demonstrated that in SZ patients, transcripts of the D3 receptor were significantly elevated, and that this 2-3 fold increase in expression was not affected by antipsychotic drug treatments (typical or atypical). Moreover, non-medicated SZ patients were found to exhibit the same patterns of gene expression, suggesting that drug treatment itself does not effect gene expression of the D3 receptor in peripheral blood leukocytes (PBLs). A similar study performed on a larger patient population both confirmed the above observation and suggested that measurement of D3 receptor mRNA may also be useful in the classification of symptom severity subgroups Kwak et al., BMC Med Genet. 2001; 2(1):3).  
      Although an early report using post mortem brains described a decrease in D 3  receptor levels in SZ brains when compared to brains from control subjects, more recent studies have suggested that in some areas of the brain the D 3  receptor levels are increased in non-medicated SZ patients, and that the elevation is reduced by neuroleptic medication (Joyce et al., Ann N Y Acad. Sci. 1999; 877, 595-613).  
      Decreases in levels of D 3  receptor mRNA in PBLs have been observed in Parkinson&#39;s disease compared to controls with similar down-regulation of D 3  receptor in Parkinson&#39;s brains (Gurlnen et al., Nature 2001; 411, 86-9, while in Alzheimer&#39;s disease (AD), a reduction of PBL dopamine D 2 -like receptors was reported (Barbanti et al., Mech Ageing Dev 2000; 120, 65-75, consistent with the levels of D 2 -like receptors in brains of AD patients, compared to control subjects. The studies lend support to use of surrogate peripheral markers in classification of psychiatric/neurological disorders, although the question remains, whether peripheral markers simply reflect brain expression levels, or alternatively may have functions in disease processes. Interestingly Levite et al. concludes from a recent study, that dopamine receptor levels on human T-cells actually reflect increased/decreased lymphocyte functionality, and report their observations that upon stimulation by a dopamine receptor agonist that mimics the effect of dopamine, the 13 receptor expression on T-cells is stimulated and results in the further activation of T-cell function (Eur J Immunol. 2001; 31, 3504-12).  
      A study of leukocyte inositol monophosphatase (IMPase) mRNA from BPD patients and control subjects showed decreased expression in BPD, with the greatest decrease observed in non-drug treated patients (Nemanov et al., Int J Neuropsychopharmcol. 1999; 2, 25-29). Additionally, a measurement and comparison of leukocyte G protein alpha subunit mRNAs in BPD patients compared with mRNA levels in unipolar patients and control subjects, showed a significant increase of transcript levels in the BPD group compared to both other groups (Spleiss, supra).  
      Results from previous studies of BPD and SZ show alterations in the concentrations of immune response mediators in blood. There also appear to be differences between the disorders in the profile and magnitude of IRS mediator changes compared to control subjects, with the literature including instances of increased serum soluble Interleukin-2 (IL-2) receptor in BPD. In SZ there is further evidence to suggest the presence of altered leukocyte gene expression (see e.g., Lin et al., Schizophr Res. 1998; 32(1), 9-15), and although there are contradictory findings and some reports suggesting that neuroleptic medication may confound these studies by causing alterations in IRS markers, the majority of the studies using neuroleptic naive or non-medicated SZ patients show IRS activation in SZ. IRS gene products reported to be up-regulated in blood from SZ and BPD patients, and that are represented on the microarrays that will be utilized in the proposed study include; IL-6, IL-1 receptor antagonist (Akiyama et al., Schizophr Res. 1999; 37(1), 97-106, IL-2 and IL-2 receptor (Tsai et al, supra). CD4, CD8, CD4/CD8 ratio, CD3 (as measured by levels of CD+ cells in blood samples) [66; 67] and TNF-α. VLA-4 receptor expression on CD4+ and CD-8+T cells was also found to be increased in SZ, and differential regulation of the IRS-associated HSP-60 and HSP-70 have been observed in patients with SZ.  
      Most recently Tang et al have used a rat model to show global gene expression changes in leukocytes, that result from experimentally induced ischemic strokes, hemorrhagic strokes, sham surgeries, kainate-induced seizures, hypoxia, and insulin-induced hypoglycemia (Ann Neurol. 2001; 50, 699-707). The specific and characteristic patterns of multigene expression observed for each experimental state lends supports to the paradigm of “surrogate markers”, where a pathological insult or process may be confined to a particular organ or process, but can induce a characteristic alteration in the overall expression profile of circulating leukocytes, thereby demonstrating that medical and neurological diseases can cause disease-specific changes to gene expression in leukocytes.  
      Example 2, supra, reports that men with SZ exhibit a characteristic pattern of leukocyte gene expression that differs from the gene expression pattern of healthy control subjects, and is diagnostic for the disease. This preliminary study generated very encouraging positive data demonstrating that eight SZ patients exhibit a leukocyte gene expression pattern that differentiates them from five healthy controls subjects. Two BPD patients were also analyzed and were shown to cluster into a subnode of the tree diagram discreetly from the SZ subjects. However, the preliminary study involved microarray gene expression analysis of only a small number of SZ (n=8), BPD (n=2), and control subjects (n=5). This Example analyzes 25 male BPD and 25 male SZ subjects.  
      Although it has been suggested that the expression of single genes could be employed for the diagnosis of psychiatric disorders such as SZ, it seems clear that the measurement of multiple gene products as markers of disease provides considerably more detailed information for diagnosis and thus a more robust classifier than single marker analysis. Significantly, Hakak et al., showed a marked improvement in the separation of SZ subjects from control subjects when many brain markers were employed for analysis (n=35), compared to analysis of few markers (n-6), following linear discriminant analysis (Hakak et al., Proc. Natl. Acad Sci U.S.A. 2001; 98: 4746-51).  
     Research Design and Methods  
      Overview. Microarray analysis measures the expression of leukocyte samples from 25 BPD and 25 SZ male patients between the ages of 25-60. Subjects are recruited from the residents of a psychiatric center and four community residential facilities. Gene expression data from the proposed study is analyzed employing hierarchical clustering, and supervised learning algorithms, and expression classifying signatures are identified (Ramaswamy et al., Proc Natl Acad Sci USA 2001; 98(26): 15149-54; Golub et al., Science; 286(5439):531-7).  
      Subject groups. Male White and African American SZ and BPD subjects are recruited into this study.  
      Medication Profiles of BPD/SZ Subjects. The BPD/SZ subjects recruited for this study primarily suffer from severe illness. In the primary study facility: (a) the SZ patient population comprised approximately, 35% paranoid, 35% residual and 20% disorganized SZ; (b) The BPD patients comprised approximately: 20% DSM 296.40 (most recent episode hypomanic), 15% DSM 296.44 (most recent episode manic, severe with psychotic features), 30% DSM 296.60 (most recent episode mixed, unspecified), 20% DSM 296.64 (most recent episode mixed, severe with psychotic features) and 10% DSM 296.80 (BPD NOS). Close to all of the patients were treated with neuroleptics during their admissions.  
      Subject Recruitment and Diagnosis. Patients are chart screened for eligibility. For patients interested in participating, informed consent is obtained in accordance with IRB regulations. Diagnostic interviews using the SCID will be conducted. The Brief Psychiatric Rating Scale (BPRS) (Overall et al., Psychol Rep. 1962; 10, 799-812) Clinical Global Impression (CGI) Mini-Mental State Exam (MMSE) (Folstein. J Psychiat Res. 1975, 12, 189-198), Scale for the Assessment of Negative Symptoms (SANS) [20-22], and Scale for the Assessment of Positive Symptoms (SAPS) will be conducted by the Research Nurse and the Psychiatrist C.I. at the patient&#39;s ward or residence.  
      Medical and Psychiatric Assessments and Exclusions. Chart records of patient subject&#39;s medical examinations including the admission examination is assessed. Medical and psychiatric history information is requested from facilities for all previously recorded admissions, for the purpose of defining a lifetime psychiatric diagnosis and to determine medical eligibility for the study. A lifetime medication history for each patient is also generated from hospital charts and records requested from other facilities.  
      A list of medical exclusions at the chart level has been generated and includes current or recent-infectious diseases, autoimmune diseases, proliferative disorders, and recent physical trauma or surgery, and chronic immunosuppressant or anti-inflammatory medication use.  
      Blood work. As part of the study procedure, CBC counts with differentials. CBC white cell counts outside of normal reference ranges, and clinically significant abnormal SMAC values or thyroid function test values will be used as exclusions.  
      Drugs screening. Results from urine screening for drugs of abuse including marijuana, cocaine, stimulants, barbiturates and heroin, performed at the time of admission are examined. Patients who test positive and those who refuse to be tested are excluded from the study. AU subjects are also questioned about cigarette smoking; number smoked/day and years of smoking are recorded. Alcohol intake and drug abuse history are also recorded.  
      Sample Collection. Fifteen ml blood samples are drawn from the antecubital vein by a study team research nurse at the patient&#39;s ward or residence. Bloods are processed immediately to isolate and purify leukocytes.  
      cRNA Synthesis and GeneChip Hybridization. High density Affymetrix GeneChip arrays were used in preliminary studies due to: 1) the large numbers of gene sequences represented within the array, 2) the highly developed protocols for probe preparation and microarray hybridization, and 3) the built-in multiple internal standards, plus custom designed normalization software for accurate comparison of results between each individual hybridizations. This latter point is of great importance, since the experimental plan involves a direct comparison between individual microarray experiments. Affymetrix Human U133A microarrays, which contain sequence-verified oligos representing nearly 20,000 individual genes, are employed to analyze gene expression signatures in blood leukocytes from the SZ and BPD subjects recruited during this study. This array is an upgraded version of the HU95A arrays employed in the preliminary studies. Both arrays contain all genes described above, and the arrays are comparable with each other. All blood samples are processed immediately following collection. All subjects samples chosen for RNA extraction are processed in duplicate, by splitting the leukocyte sample extracted from whole blood and processing them identically thereafter.  
      Replicate Sample processing. The need for replicate microarray experiments is axiomatic. Sources of variation and necessary levels of replication vary considerably among the different array platforms, however Churchill has suggested that many considerations are applicable to both cDNA and oligo platforms. The term biological replication can have two meanings; “actual biological replication” is replication of array processing and hybridization, involving mRNA from different extractions from the same sample or individual, and “biological replication” where target mRNA comes from different versions of a cell line, or different individuals. These forms of replication are very different in nature, with the latter involving a much greater degree of variation in measurements. Several reasons for performing actual biological replication have been suggested; this replication provides an estimate of the experimental reproducibility, it permits the identification of “bad” arrays, and actual biological replication can improve precision of the expression profile for a given RNA sample though the averaging of multiple arrays. Replicate samples are also extremely useful when attempting to establish that a disease classification is robust, which is particularly true for class discovery algorithms where the large number of genes make it relatively easy to discover interesting patterns of expression, even in random datasets. Each subject was processed in duplicate, and perform actual biological replications. The above considerations, in particular that the robustness of the classification is deemed essential, coupled with the reproducibility of Affymetrix arrays, hybridization protocols and scanning (mean r2=0.967 for repeat experiments justifies the use of duplicate sample processing.  
      Data Analysis. Affymetrix Software Suite is employed for image acquisition and normalization of the fluorescent signals. Analysis of signal intensities over each probeset within each experiment will fall into two main categories; Hierarchical Clustering (see e.g., Alizadeh et al., Nature 2000; 403(6769):503-11) and Supervised Learning Algorithms (Ramaswamy et al., supra). In addition, group difference testing is performed using SAS GLM procedures, including multivariate analysis of variance (MANOVA), used to test factors such as smoking status and medications as confounds in the group analyses. Finally, in the preliminary analysis a permutation analysis was employed to assess the subject cluster reliability. A Bootstrapping Cluster analysis will be implemented for reliability investigations.  
      Hierarchical Clustering. A hierarchical clustering algorithm Eisen et al., Proc Natl Acad. Sci. 1998; 95(25):14863-8), has been successfully applied to classify gene expression data (Alizadeh et al., supra), and is described in Example A, supra. Specifically, a Student&#39;s two-tailed t-test is performed across the genes expressed in the subjects leukocytes, and then employed Cluster to perform a supervised analysis on the genes found to be differentially expressed (p&lt;0.1), resulting in firstly a classification of SZ and control subjects into their respective groups, and then a classification of BPD from SZ subjects. For this Example, these and other analysis of variance procedures are used for supervised cluster analysis of SZ and BD. The resultant clusters will represent multigene expression signatures specific for the diagnosis and that are useful for testing classification.  
      Supervised Learning Algorithms. Supervised learning algorithms are described in detail in Example A, supra.  
      Validation Using Quantitative RT-PCR. Microarray data are validated by real-time RT-PCR on genes randomly chosen from those observed to be differentially regulated among leukocytes obtained from psychiatric patients. Gene-specific primers are designed and employed for the SYBR Green PCR assay. Specifically, reverse transcribed cDNA is processed in duplicate from each patient RNA sample. Real-time PCR assays are then performed in triplicate for each cDNA sample. This experimental replication allows accurate confirmation and validation of the expression data from microarray analysis.  
      Additional Approach to the Development of Multigene Expression Signatures. The Affymetrix GeneChip human U133 series contains a second U133B array, with an additional 15,000 oligo sequences derived from characterized genes and non-redundant EST sequences. Use of this second array may extend the analysis with the aim of increasing the complexity of leukocyte specific multigene signatures.  
      This Example results in the creation of leukocyte multigene expression signatures that can classify leukocyte samples by the patient diagnostic groups (BPD and SZ), and that can be used to predict the class of unknown samples. Recruitment of additional patients from the subject groups ultimately allows the power of the expression signatures to be calculated. SZ and BPD-specific expression multigene expression signatures can be generated from multiple racial groups and female subjects, and further studies can determine the ability to assess or predict patient response to treatment based on leukocyte multigene expression signatures measured at admission, and/or by collection of longitudinal expression profile data following patient admission and during treatment, to determine correlates of treatment response. A longitudinal study of families with members at increased risk of developing psychiatric disorders because of illness in other family members can be performed. Gene expression patterns can be detected that classify psychiatric patients by diagnosis, are present in premorbid/prodromal subjects, and establish whether it is possible to predict risk of psychiatric illness from prodromal samples, potentially allowing for targeting of treatment to at-risk individuals such as those with schizotaxia. Disease-specific classification of psychiatric illness has multiple clinical uses, such as a diagnostic support to the psychiatrist on initial presentation of the patient. Also of major importance for psychiatric genetics research, multigene signatures can be employed to assay members of large SZ and BPD pedigrees employed for genetic linkage studies. Affected members, having an accurate biological classification of diagnosis, may help to avoid compounding errors in linkage studies.  
     Example 6  
     Schizophrenia Diagnosis with Leukocyte Multigene Signatures  
      This Example generates gene expression data from neuroleptic naive schizophrenic patients, in order to avoid the potential confounder of neuroleptic drug-derived gene expression changes. Additionally, an increased number of chronic neuroleptic-treated schizophrenics and healthy control subject&#39;s cases are tested in the gene expression dataset. The data generated in this proposed study, along with previously collected data, permit classifying multigene expression profile, using hierarchical clustering and supervised learning algorithms, that can correctly distinguish leukocyte gene expression levels of schizophrenic patients from control subjects. This in turn provides diagnostic information from leukocyte multigene signatures and defines those at risk for SZ development. This also establishes the ability to develop multigene expression signatures for other psychiatric disease.  
     Background  
      Example 2, supra, generated very encouraging positive data demonstrating that SZ patients exhibit a leukocyte gene expression pattern that differentiates them from controls.  
      However, this study involved microarray gene expression analysis of only a small number of schizophrenic patients (n=8) and control subjects (n=5). This Example analyzes 32 male schizophrenic patients and 14 control male subjects, from multiple ethnic groups. Furthermore, the eight schizophrenic patients analyzed in the preliminary study had medication profiles that were diverse and included several different classes of atypical and typical neuroleptic medications: Subject 493: Olanzapine, Depakote, Risperidone., Subject 494: Chloral Hydrate, Zyprexa., Subject 495: Loxapine, Benztropine, Seroquel, Vistaril., Subject 535: Clozapine, Artane., Subject 588: Haloperidol, Haloperidol Decanoate, Cogentin, Depakote., Subject 630: Olanzapine, Risperidone., Subject 631: Haloperidol, Clozapine. There is growing evidence supporting disease specific alterations of leukocyte gene expression in SZ, but it has also been shown that neuroleptic medications can disturb IRS mediator concentrations in blood (Muller et al., Eur Arch Psychiatry Clin Neurosci 1997; 247: 308-13)].  
      In order to prove the presence of a signature, this Example performs the multigene expression analysis of neuroleptic naive schizophrenics, employing data analysis algorithms that identify common gene expression signatures between naive, and medicated SZ subjects, that can be utilized for classification of SZ subjects from healthy control subjects.  
      Measurement of Multiple Markers. Although it has been suggested that gene expression could be employed for the diagnosis of SZ using a single marker (Ilani et al., supra)], it seems clear that the measurement of multiple gene products as markers of SZ provides considerably more detailed information for identification of the disease and thus a more robust classifier than single marker analysis. Significantly, Hakak et al., supra, showed a marked improvement in the separation of SZ subjects from control subjects when many brain markers were employed for analysis (n=35), compared to analysis of few markers (n-6), following linear discriminant analysis. The use of multiple markers may in future also, e.g. allow the classification of biological subgroups of schizophrenic patients who respond to different treatments.  
      mRNA levels quantified by RT-PCR techniques is extremely time-consuming if many genes are analyzed in one experiment. By employing microarray technology, mRNA levels of thousands of genes expressed in peripheral blood leukocytes can be quantified, including genes coding for all of the markers described above. Global differential gene expression measured using the microarray approach identifies patterns or signatures of gene expression that differ between schizophrenic patients and control subjects, and thus form the basis of the diagnostic technique.  
     Research Design and Methods  
      Overview. Microarray analysis measures the expression of leukocyte samples from 20 neuroleptic-naive SZ patients, 12 medicated SZ patients and 14 age-matched control subjects. Neuroleptic naive subjects are recruited from an urban emergency room. The study team clinical staff obtains informed consent, and a 15 ml blood sample is collected from each subject prior to a first neuroleptic dose. Blood samples are processed to isolate and purify the leukocytes and the samples are then stored. Patient notes and admission and discharge diagnoses are reviewed by the study team after twelve weeks, and samples from patients who have a confirmed SZ diagnosis will be further processed for microarray expression analysis. Neuroleptic-treated SZ patients are recruited from the residents of a psychiatric facility or community residential facilities. Control subjects are recruited from the staff. Gene Expression data from the proposed study are collated with the existing preliminary study data, and analyzed employing analysis of variance procedures, hierarchical clustering, and supervised learning algorithms.  
      Neuroleptic-Naive Schizophrenic Patients. Twenty neuroleptic naive SZ patients between the ages of 21-65 are completed during this study. Patients presenting at an ER are screened for inclusion in the study. It is estimated, that up to about 50% of the neuroleptic naive subjects initially considered to have SZ and recruited into this study, may later be diagnosed as having disorders other than SZ. Potential subjects are thus recruited and blood samples drawn but not processed to completion until retrospective formal diagnosis by the study team.  
      Subjects are recruited based on their initial psychiatric evaluation performed by a resident psychiatrist and nurse. For patients interested in participating, informed consent is obtained in accordance with regulations. The neuroleptic naive status of candidate patients is ascertained from a combination of sources including patient&#39;s report of their own status, and other significant sources such as patient&#39;s family member reports, and/or psychiatrist or therapist reporting from private care or if they have been outpatients at other facilities, and other collateral information. Patient&#39;s initial medical examination information is used to determine general health. Medical exclusion information for this study are ascertained by questioning of the subject and from family members and/or other collateral information. Medical exclusions include current or recent-infectious diseases, abnormal CBC counts, autoimmune diseases, proliferative disorders, and recent physical trauma or surgery, chronic immunosuppressant or anti-inflammatory medication use.  
      Retrospective Neuroleptic-Naive Subject Diagnosis. The initial SZ diagnosis given to a proportion of neuroleptic naive subjects who are recruited into this study could be changed during the course of their admission. In order to maximize the number of microarray-analyzed samples from subjects who are correctly categorized as SZ, initial blood processing on all neuroleptic-naive patients who carry either a SZ diagnosis or a “rule-out” SZ diagnosis, following initial assessment and SCID diagnosis, is performed. This initial process includes the isolation and purification of the leukocytes, and storage of samples at −70° C., which ensures RNA stability for &gt;6 months (Qiagen). The study team reviews subject&#39;s notes and diagnosis twelve weeks after the subject&#39;s admission. This time period will allow for a fuller set of notes to be created, and also for acquisition of patient notes and history from any other sources or institutions. Additionally, if a subject has been discharged, his discharge diagnosis and summary are present/available in the notes. Following this retrospective confirmation of subject&#39;s diagnosis, 20 subjects were selected for GeneChip analysis.  
      Neuroleptic-Treated Schizophrenic subjects. Twelve male neuroleptic-treated SZ subjects between the ages of 21-65 are completed in this study. Subjects will be recruited from a psychiatric center and community facilities. Male residents of the five facilities are screened. Exclusions at the chart level will include a diagnosis other than SZ. Patients are interviewed as to their interest in participating in the study and informed consent is obtained in accordance with IRB regulations. Records from previous hospitalizations are obtained and also used to confirm the schizophrenia diagnosis. Medical exclusions will be identical to those described for neuroleptic naive patient.  
      Schizophrenia Diagnosis of Subjects. A psychiatric diagnostic and assessment interview is conducted by the study team using the SCID [5] in order to confirm the RPC chart diagnosis (neuroleptic-treated) or initial ER assessment (neuroleptic-naive) diagnosis for each subject. Patient records from previous treatment providers are obtained and also used to confirm the psychiatric diagnosis. Diagnostic interviews for the SCID will be conducted by the SCID trained members of the study team and the research nurse who is also SCID trained and certified. For neuroleptic-naive subjects, initial SCID diagnosis is retrospectively compared to subject&#39;s notes after 12 weeks, and only samples from subjects where there is agreement between the sources will be further processed for GeneChip analysis.  
      The Brief Psychiatric Rating Scale (BPRS), Clinical Global Impression (CGI), Mini-Mental State Exam (MMSE), Scale for the Assessment of Negative Symptoms (SANS) (Andreasen et al., Br J Psychiatry 1989; Suppl (7), 49-58. 89), and Scale for the Assessment of Positive Symptoms (SAPS) (Andreasen et al., Psychopathology 1995; 28: 7-17) are conducted by the study team or research nurse during the diagnostic and assessment interview. These scales are used to assist in the diagnostic process and to descriptively characterize the subjects.  
      Drugs Abuse Screening. Results from comprehensive urine screening for drugs of abuse including marijuana, cocaine, stimulants, barbiturates and heroin, performed at the time of admission or on the day of the study blood draw will be examined. Patients who refuse to be tested are excluded. Subjects are also questioned about cigarette smoking and number of cigarettes smoked per day.  
      Control Subjects. Fourteen male control subjects aged 21-65 are recruited from staff. The ages of the control subjects completed are defined by the patient sample and adjusted to maximize the similarity in ages between the groups. Controls complete a form (with the assistance of the study team) documenting that neither they nor their first degree relatives have a history of SZ, other psychotic disorders, mood disorders or of paranoid, schizoid, or schizotypal personality disorder. Current medication use and medical history are recorded. Medical exclusions are identical to those described for neuroleptic naive patients.  
      Blood Sample Collection, cRNA Synthesis and Hybridization. A fifteen ml blood sample is drawn from the antecubital vein by a phlebotomist or nurse. A CBC is performed on each blood sample. Blood is processed immediately to isolate and purify leukocytes, stored at 70° C. and stored for further processing. Leukocytes are extracted from blood samples immediately following collection. The leukocytes are stable at −70° C. (&gt;6 months, Qiagen), and storage at that temperature allows the retrospective determination of which samples are to be hybridized to GeneChips, after a detailed analysis of all available patient history and a confirmed diagnosis of SZ. Samples chosen for RNA extraction are processed in duplicate, by splitting the extracted leukocyte samples and processing them identically thereafter. High density Affymetrix GeneChips and data analysis are described in Example 3.  
      Quantitative RT-PCR. Microarray analysis data are validated performing real-time RT-PCR on genes randomly chosen from those observed to be differentially regulated among leukocytes obtained from SZ patients and controls. Gene-specific primers are designed and employed for the SYBR Green PCR assay. Specifically, reverse transcribed cDNA is processed in duplicate from each patient RNA sample. Real-time PCR assays are then performed in triplicate for each cDNA sample. This replication should allow accurate confirmation and validation of the expression data from microarray analysis. This Example provides a leukocyte multigene expression signature that can classify leukocyte samples into SZ patient or control subject groups, which can be used to predict the class of unknown samples. A multigene expression signature that classifies leukocyte samples from both neuroleptic naive and medicated SZs is necessary because drug induced changes to gene expression patterns are a potentially confounding factor and may mask the disease specific signature for SZ. Recruitment of additional patients from all subject groups, and the inclusion of female subjects, ultimately will allow the power of the expression signatures to be calculated. This is facilitated by ongoing interactions with clinicians at all study sites, and should greatly facilitate the ultimate clinical application of the results.  
      This Example further establishes the ability to develop a database of specific leukocyte multigene expression signatures for other psychiatric disorders including bipolar disorder, schizoaffective disorder and major depression, which will in turn permit biological diagnosis of psychiatric patients. A longitudinal study, recruiting families with members at increased risk of developing SZ because of illness in other family members, is possible.  
     Example 7  
     Alzheimer&#39;s Disease Diagnosis with Leukocyte Multigene Signatures  
      The NINCDS-ADRDA and DSM-IV criteria are currently widely used for diagnosis of probable Alzheimer&#39;s disease (AD). These clinical criteria have a number of limitations, including lack of specificity and sensitivity in the diagnosis, and have an error rate of about 10% even in academic research centers. Furthermore, diagnosis based on cognitive function can only be made post symptomatically, at which time medications that may inhibit AD development or delay its progression will likely be ineffective. The imaging and biological marker diagnostic methods currently under development have additional drawbacks in terms of their need for highly specialized equipment, and specificity and sensitivity respectively, and thus may not be useful for early screening.  
      The present Example produces pilot data for development of a biological classification of AD patients, based on high-density microarray measurement of transcribed white blood cell (leukocyte) RNA. The rationale behind this proposal is based on two sources of data: 1) Current scientific literature, in which there is growing evidence that individuals with AD exhibit immune and other responses, that can be detected at the level of altered gene expression in circulating peripheral leukocytes. Quantitation of the mRNA transcripts in leukocytes of a number of individual genes has demonstrated associations between gene expression levels and the presence of AD. 2) Preliminary results from a microarray study by the PI, investigating gene expression changes in men with schizophrenia (Example 2, supra). Initial results from this expression study have been striking: supervised cluster analysis of peripheral leukocyte gene expression data, using transcript level measurements of thousands of genes from seven schizophrenic patients and five matched control subjects, resulted in a classification of all the subjects into their correct group. These results provide evidence to suggest that a surrogate tissue can be successfully employed for classification of a neuropsychiatric disease.  
      Utilizing a similar microarray strategy, this Example shows that individuals suffering from AD exhibit a conserved pattern of gene expression levels in their peripheral blood leukocytes, which is distinct from the pattern of expression in peripheral blood leukocytes from control subjects. This study provides a clinical assay that is minimally invasive, and has the capacity to identify AD sufferers, and can also provide important pre-symptomatic and early stage diagnostic information.  
     BACKGROUND  
      Alzheimer&#39;s disease (AD) is the most common cause of degenerative dementia, representing about 65% of cases and affecting about four million Americans. Increased life expectancy, especially in the developed world has been accompanied by large increases in the AD rate, as its prevalence appears to double for every five years of age increase (Katzman et al., (2001) In Iqbal, K., Sisdia, S. S., and Winblad, B. (eds), Alzheimer&#39;s Disease: Advances in Etiology, Pathogenesis and Therapeutics. John Wiley and Sons, Ltd. Chichester, England, pp. 11-21). AD is believed to have a long preclinical phase, followed by a mild cognitive impairment (MCI), characterized by mild memory loss. AD dementia then follows with progressive deficits across multiple cognitive domains, including attention, memory, verbal ability, visuospatial skill, problem solving and reasoning, and along with stroke may be the third most common cause of death in the U.S. (Ewbank et al., Am J Public Health 1999; 89: 90-92). The growing economic and social costs of AD have made it a major public health issue, and prompted intensive study of its etiology and pathogenesis in order to facilitate development of preventative and therapeutic treatments.  
      Susceptibility to AD has a significant genetic component, and the discoveries of presenilin 1 and 2 (PS1, PS2), and amyloid precursor protein (APP) gene mutations that result in the familial forms of AD (early onset), have helped to elucidate the disease etiology Tandon et al., Genome Biol. Reviews 2002; 3: 3014). However, familial AD accounts for only approximately 2% of all AD cases and although genetic risk factors for sporadic AD have been identified, for example the presence of the epsilon 4 allele of Apolipoprotein E (APOE4) (Farrer et al., JAMA 1997; 278: 1349-56), many cases of AD do not carry the APOE4 allele and have no known associated gene mutations. Therefore the remaining genetic effect in AD has yet to be identified, and likely involves several genes of small effect. There are major efforts underway to find genes that play a role in the development of the sporadic AD, through linkage analysis and association studies.  
      Several chromosome regions and many potential genes, including the TNF-alpha and the estrogen receptor alpha genes have been suggested as possible candidates, although there are some concerns with candidate gene association reproducibility.  
      Epidemiological studies have begun to show that early detection and treatment of AD may be associated with a more favorable outcome, involving both overall risk and also progression and severity of disease. A biological assay providing information that could help identify and classify AD and define susceptibility at an early stage, especially in high-risk families, could provide a great public health benefit. Such an assay would potentially allow for targeted treatment strategies to commence before the onset of many symptoms. Recent studies have also indicated the need for early and accurate differential diagnosis of AD from other dementias.  
      Diagnosis of AD is commony performed using the NINCDS-ADRDA and DSM-IV criteria with direct patient assessment and interviews with family members. The criteria can provide a diagnosis of probable AD primarily based on cognitive function. Dementia severity can also be stratified according to the Mini-Mental State Examination (MMSE). Unfortunately, these diagnostic tools are inadequate for early diagnosis of abnormal changes in the brain that likely began long before cognitive impairment. Thus, even though highly skilled and experienced practitioners in a research center setting can achieve about 90% accuracy in patients meeting clinical criteria for dementia, several studies have documented the high levels of unrecognized dementia in the general community (Galasko et al., Arch Neurol 1994; 51: 888-95). In addition, it has also been shown that the clinical criteria are unable to predict neuroimaging findings, suggesting that brain imaging is currently necessary in the diagnostic evaluation of dementia (Chui et al., Neurology 1997; 49: 925-35). In order to improve the specificity of AD diagnosis and to develop pre-symptomatic and early stage diagnosis, neuroimaging (e.g., magnetic resonance imaging (MRI), positron emission tomography (PET), and single photon emission computed tomography (SPECT)) and biological marker detection techniques are under investigation in many studies. A few of these new methods and assays are described and the potential benefits and problems associated with each are discussed below.  
      Using fMRI, Bookheimer et al reported an increased magnitude of and extent of brain activation in the hippocampus, parietal and prefrontal cortex during a challenging memory test in subjects with the APOE4 allele, compared to those without an APOE4 allele, and concluded that during performance of a memory task, persons at risk of developing AD have preclinical compensatory increases in blood flow to those regions (Bookheimer et al., N Eng J Med 2000; 343: 450-6). However, neuroimaging techniques are sophisticated and relatively expensive, and require a high degree of operator skill and interpretation. Implementation of these methodologies into the general clinical setting may prove difficult, and even in specialist centers evaluation may take several hours of patient and clinician time. Additionally, it is expected that an increase in current specificity and sensitivity of the techniques may require further development for practical use  
      Methods for the early detection, and diagnosis of AD by measurement of biological markers in CSF are currently under development and include measures of Aβ, tau and phosphorylated tau proteins, as they are intimately involved in the senile plaques and neurofibrillary tangles of AD. CSF levels of Aβ are decreased, and levels of tau and phosphorylated tau are increased in AD. However, their levels are variable and neither has the sensitivity and specificity for routine use or for screening CSF-derived measurements of biomarkers requires that patients to undergo a lumbar puncture. The requirement for a lumbar puncture, which is a fairly invasive procedure that causes some discomfort, would probably mean a CSF-based assay would be unsuitable for population screening and for future pre-symptomatic detection of AD.  
      In a large study of non-demented-, non-AD demented-, and possible or probable AD-subject groups, utilizing urine AD7C-NTP measurements, Munzar et al showed significant differences between the subject groups. There was however, considerable overlap in urinary AD7C-NTP levels between the groups, showing a lack of specificity (Munzar et al., Neurol Clin Neurophysiol 2002; 2002: 2-8).  
      Measurements of Aβ42 in non-demented elderly subjects showed that, after 3 years, however, only those with upper quartile levels of Aβ42 were significantly more likely to develop AD than those in the lowest quartile (Mayeux et al. Ann Neurol 1999; 46: 412-16). However, other studies have found inconsistent findings.  
      Serum Melanotransferrin (P97) was assayed in a group of possible and probable AD subjects, and healthy controls and significantly higher P97 was found in the possible/probable AD group, although there was overlap between the subject groups (Feldman et al., J Alzheimers Dis 2001; 3: 507-16). In a similar study, Kim et al. measured serum P97 in controls, and AD and non-AD dementia subject groups and reported a significant difference between the AD group and the non-AD and normal control groups (also with the AD group elevated compared to the others), but no significant difference between the non-AD dementia group and the control group. α-1 antichymotrypsin (ACT) levels were measured in serum from AD, VD, and healthy control subjects and were found to be significantly higher in the AD group than the other two groups, although ACT levels in the VD and control groups showed no difference. However, a lack of specificity of serum marker was inferred by the overlap between subject groups.  
      Tan et al. measured the CD45RO and CD45RA isoforms of CD45 on T-cells from AD, MCI, non-AD dementia, and age matched healthy control subject groups. They found significantly lowered CD45RA and increased CD45RO/CD45RA ratio in the AD patient group and in the MCI group, compared to the healthy control subjects. The non-AD dementia group did not differ significantly from the healthy control group, and there was considerable overlap in the CD45 isoform levels between the subject groups.  
      Currently the CSF assays for Aβ and Tau have problems of specificity and sensitivity due to highly variable levels in CSF samples. Additionally, diagnostic assays requiring CSF samples are relatively invasive, would cause patient discomfort, may need a hospital setting and may require patient sedation. These factors may discourage use of CSF-based assays for population and pre-symptomatic screening, even if the assays themselves are improved. Although minimally invasive, the blood, blood-fraction and urine-based AD biomarker assays under development also have a relative lack of specificity.  
      Current antemortem AD diagnosis has variable accuracy and only produces a probable diagnosis. There is therefore a need for a sensitive and specific biological assay for AD diagnosis that can be performed using an accessible tissue, at relatively low cost, and without the requirement for sophisticated equipment at the site of sample collection. This would allow for regular screening of pre-symptomatic subjects, and could also be used to assess the effectiveness of medications in the prevention and/or delay of symptoms.  
      To date, published microarray analyses of AD have focused on analysis of post mortem brain tissue to investigate the etiology of AD. Areas of the brain affected by the progression of the disease have been studied with exciting early results. Using cDNA microarrays, Hata et al. identified genes found to be differentially expressed between AD brain hippocampus and parietal cortex (but not differentially expressed in control subjects brain), and suggested that these genes may be regulated in response to neurofibrillary tangle-related destruction and are thus potential therapeutic targets (Biochem Biophys Res Comm 2001; 284: 310-16). Further dissection of the hippocampus was performed by Colangelo et al., who employed Affymetrix arrays to identify gene expression specific to AD in the hippocampal cornu ammonis 1 (J Neurosci Res 2002; 70: 462), while Loring et al., investigated expression in AD cingulate and amygdala brain sections (DNA Cell Biol. 2001; 20: 683). Strikingly similar results were reported from both studies, including the generalized depression in brain gene transcription, decreases in many known transcription factors, neurotrophic factors, and signaling elements involved in the synaptic pathway and also the up-regulation of genes involved in inflammatory, stress and immune and responses. These experiments have thus employed a global gene expression analysis to validate several theories of AD pathology and have identified pathways for future drug targeting.  
      Although microarray analysis of brain samples has and will provide important information on the etiology and pathogenesis of AD in brain tissue, it is obvious that use of brain samples from living patients for molecular diagnostic classification is not feasible. Thus, the development of any multigene expression-based classification of AD should focus on a tissue that is accessible. Peripheral blood samples are easily obtained and most significantly, it has previously been reported that patients with AD have altered levels of multiple gene products that are expressed in blood leukocytes.  
      In a recent study, Schipper et al. measured plasma levels of HO-1 protein in early sporadic AD, normal elderly control (NEC), normal younger control, age-associated cognitive decline (AACD), non-AD dementia, non-dementing neurologic illness and chronic medical disorder groups of subjects (Neurology 2000; 54: 1297-1304). The authors found that compared to the NEC group, the AD group had significantly lower HO-1 protein levels. Lymphocyte HO-1 mRNA levels were also measured for each subject, and were found to be significantly lower in AD relative to NEC, and levels were also found to be decreased compared to the AACD, non-AD dementia, non-dementing neurologic illness, and chronic medical condition groups. In addition, HO-1 mRNA levels were also lower in the AACD group compared to the NEC group suggesting a use for this transcript as a peripheral marker of both AD and age-associated cognitive decline. Transcript levels of the heat shock protein HSP-70 were also reported as a potential marker for AD. mRNA levels of HSP-70 in mononuclear blood cells were measured by Northern blot analysis, and although no correlation was observed between HSP-70 and aging, mRNA levels were found to be significantly lower in AD patients when compared to both VD patients and non-demented control subjects. In addition to the reports described above, further evidence for differential gene expression in AD leukocytes comes from multiple studies describing changes in the immune system in AD patients that result in abnormalities of peripheral blood lymphocytes, such as the multiple increases in circulating and in-vitro produced cytokines including CD4, CD25, and CD28 antigen, and decreases in CD7 and CD8, and the increase in T-lymphocyte IL-6 receptor 62. It therefore seems likely that for multiple genes, differential gene expression will be associated with the alteration in T-cell phenotype and dysfunctional immunity in AD.  
      Example 2, supra, reports that men with schizophrenia (SZ) exhibit a characteristic pattern of leukocyte gene expression, that differs from the gene expression pattern of healthy control subjects, and would thus be diagnostic for the disease. This study has generated very encouraging positive data by demonstrating that SZ patients exhibit a leukocyte gene expression pattern that differentiates them from controls. In addition, the seven schizophrenic patients analyzed in the study had medication profiles that were diverse and included several different classes of atypical and typical neuroleptic medications, providing some evidence to suggest that SZ subject classification from control subjects is not directed by a specific medication profile. As reported below, these studies now include the analysis of additional subject numbers, including neuroleptic naive SZ subjects, to allow further development of a SZ leukocyte classifier. Data for comparison of multigene expression signatures between different psychiatric disorders are being generated. One major depression patient and two bipolar disorder patients, all of whom were receiving neuroleptics are recruited. Preliminary cluster analysis of leukocyte gene expression data showed a distinct separation of the bipolar and major depression subjects from SZ subjects, with an internal separation of bipolar from major depression. This data does show that the leukocyte expression signatures are disease specific and can be used to classify between different neuropsychiatric disorders.  
      Although it has been suggested that gene expression could be employed diagnostically for AD, using single markers, it seems clear that the measurement of multiple gene products as markers of AD provides considerably more detailed information for identification of the disease, and thus a more robust classifier than single (or dual) marker analysis. A recent investigation on SZ supports this assumption; Hakak et al., showed a marked improvement in a brain expression classification of SZ subjects from control subjects when many brain markers were employed for analysis (n=35), compared to analysis of few markers (n-6), following linear discriminant analysis.  
     Design and Methods  
      Overview. Microarray analysis measures the expression of leukocyte samples from 20 AD patients and 20 age-matched healthy control subjects. The study team obtains informed consent, and a 15 ml blood sample is collected from each subject prior to initial medication. Blood samples are processed to isolate and purify the leukocytes and the samples are stored prior to RNA purification, cRNA synthesis and GeneChip hybridization and scanning. Gene Expression data is analyzed by ANOVA testing, and by employing hierarchical clustering, and supervised learning algorithms.  
      Subject groups. Male AD patients and control subjects from all ethnic groups are recruited. There have been multiple reports in the literature of the ability of microarray analysis to accurately classify disease tissues even though micro-dissection was not performed to remove multiple non-disease cell types within the tissue. Additionally, a recent report illustrated a classification of leukemia when whole blood was employed for initial RNA extraction (Armstrong et al., Nat Genetics 2002; 30: 41-47). These papers suggest that the algorithms employed to determine signatures of gene expression are not confounded by either complex tissues (with only a sub-section containing the cells of interest), or inter-subject variation of genes in total peripheral blood. It is unlikely that expression variability due to ethnicity will mask an AD-specific leukocyte multigene expression signature.  
      Recruitment of AD Patients. AD subjects are recruited based on their initial evaluation and a diagnosis of probable AD. Candidate patients are approached and interviewed as to their interest in participating in the study. For patients interested in participating, informed consent is obtained. If possible, recruitment is limited to patients who have not yet received medication for AD, however medicated patients may be recruited into the study to ensure completion. Evidence from the SZ studies (Example 2, supra) suggest that neuroleptic medication does not primarily direct and/or mask leukocyte classifiers of disease. In addition, and if necessary for the AD research, subjects receiving a diverse range of medication treatments are recruited. This approach will decrease the likelihood that detected gene expression patterns are induced by a specific medication.  
      Patient&#39;s initial medical examination information is used to determine general health. Medical exclusion information for this study is ascertained by questioning of the subject and from family members and/or other collateral information. Medical exclusions include current or recent-infectious diseases, autoimmune diseases, proliferative disorders, and recent physical trauma or surgery, chronic immunosuppressant or anti-inflammatory medication use. Patients with CBC white cell counts outside of normal ranges are also excluded.  
      These selection and exclusion criteria have been designed to reduce the likelihood of detecting AD leukocyte gene expression patterns that differ from matched control subject gene expression patterns, but that arise not from the disease process but from other factors such as medication or the presence of an infectious agent.  
      Male Control Subjects. Twenty male control subjects are recruited from the staff and the local community. Subjects are in the age range of 65 and older. Control subject age is defined by the patient sample as the ages of the control subjects are adjusted to meet the mean age of the patients, so as to maximize the similarity in ages between the groups. Thus control subject recruitment is initiated following the completion of AD subject recruitment. Control subjects are asked to complete a form documenting that neither they nor their first-degree relatives have a history of AD. Forms are also completed listing current medication use and medical history. Medical exclusions are identical to those described for AD patients above.  
      Blood Sample Collection. Fifteen ml Blood samples are drawn from the antecubital vein. A CBC is performed on each blood sample. Bloods are processed immediately to isolate and purify leukocytes, and stored for further processing.  
      Quantitative RT-PCR. Microarray analysis data are validated as described above by performing real-time RT-PCR on genes randomly chosen from those observed to be differentially regulated among leukocytes obtained from AD patients and controls. This Example results in the creation of a leukocyte multigene expression signature that can classify leukocyte samples into AD patient or control groups and can be used to predict the class of unknown samples (using a supervised learning approach). Recruitment of additional patient and control subjects and the inclusion of female subjects, allows the power of the expression signatures to be calculated. The data generated from this work permits investigation of the specificity of the multigene expression signatures by generating expression signature data for different forms of non-AD dementia. Longitudinal studies can be designed to generate multigene expression pattern data from pre-clinical subjects at risk of AD (through familial mutations or APOE4 alleles), and to investigate the feasibility of early diagnosis of AD utilizing multigene expression signature data.  
      Gene expression patterns that classify AD patients can be determined to be present in subjects prior to the onset of symptoms. It is thus possible to predict risk of AD from pre symptomatic subject&#39;s samples, potentially allowing for targeting of treatment to at-risk individuals.  
      A diagnosis of AD with improved specificity and sensitivity has multiple clinical uses, such as a diagnostic support to the clinician on initial presentation of the patient. Also of major importance for AD genetics research, multigene signatures could be employed to assay members of AD pedigrees employed for genetic linkage studies. Affected members, having an accurate biological classification of diagnosis may help to avoid compounding errors in linkage studies.  
     Example 8  
     Detection of Genetic Alterations Through Gene Expression in Surrogate Samples  
      Surrogate tissue can also be used to identify genetic defects or sequence alterations, such as mutations or polymorphisms, associated with, or resulting in, or contributing to, a physical state or susceptibility to a physical state. Genes/ESTs/sequences are shown to have altered expression in a surrogate tissue between the “disease” and “healthy” samples or subjects, and are potential candidates for having DNA mutations or alterations such as polymorphisms, that are related to the disease or physical state of interest.  
      The benefit of this objective is that it will necessitate sequencing of a smaller number of genes, to identify candidate “disease” genes, than currently used in other methods for discovering “disease” genes. Also, use of the present method for analysis of gene expression in surrogate tissues (e.g., blood leukocytes) allows freedom of subject choice, and in the case of SZ, does not require access to postmortem brain tissue, or tumor biopsy tissue for the identification of susceptibility genes for cancer development.  
      This method can be employed for any physical state with a genetic component. Specific applications for SZ and prostate cancer are outlined below in Examples 8A and 8B. A list of candidates for further examination for prostate cancer is provided in Example 8B.  
     Example 8A  
     Schizophrenia  
      Schizophrenia (SZ) is a complex disorder with a high heritability and approximately ten-fold increased risk in first-degree relatives. Genome scans are widely used in the search for SZ linkage regions, as prerequisite for identification and mutation screening of candidate SZ susceptibility genes. Studies to date possess a number of limitations, including lack of reproducible, strong linkage findings, and the large breadth of chromosomal areas identified, which can contain potentially hundreds of genes.  
      It is also believed that multiple genes of small or moderate effect may contribute to SZ susceptibility, and therefore need to be identified within the linkage regions. However, linkage studies have highlighted a number of chromosomal regions that may harbor genes that contribute to SZ. The difficult task is to identify susceptibility alleles among the large numbers of genes within these regions. Sequence analysis and association testing for all the genes within regions of linkage would be an overwhelming task and a more focused approach for candidate gene identification of is required. One embodiment of this method is designed, based on integration of linkage and gene expression data, for discovery and validation of SZ candidate genes.  
      Feasibility of this embodiment of the method was investigated using preliminary study gene expression measurements (from Example 2 above) of about 12,000 genes and ESTs from eight SZ patients and five control subjects (CS).  
      These preliminary study findings were very positive: 9774 genes and ESTs were mapped to the genome, and sorted and ranked by significance level of differential expression. In this particular example, genes were considered to be “expressed” if they had a GeneChip intensity of ≧100 intensity units (IU) (intensity values that were calculated through Affymetrix MAS 5.0 from a scaling factor of 100 for the data), and 1042 of the mapped, “expressed” genes were differentially expressed (p&lt;0.05) between the eight SZ subjects and five healthy CS groups (note that use of an additional SZ subject has increased the number of genes found to be significantly differentially expressed from that described in Example 2).  
      Mapped-gene expression data were then filtered using increasing GeneChip intensity thresholds, and the ten top ranking genes were each scored as mapping either to a region of SZ linkage (1), or to another genome region (O). The ten top ranked gene&#39;s scores were summed and recorded. When all mapped genes were included in the analysis (zero intensity filter) 2/10 genes fell within a region of linkage. A filter of increasing expression level stringency was applied in 20 IU increments, excluding genes for which less than two subject&#39;s IU values equaled or exceeded the IU threshold for that gene. Thirty complete, independent sets of randomized mapping data were generated and used to determine the frequency of random gene mapping to a linkage region.  
      For the real GeneChip expression data, when the IU cutoff reached 100, the number of linked genes climbed from 2/10 to 4/10. This was of interest because it was considered that GeneChip IU levels ≧100 indicated real gene expression, rather than background signal. As the IU filter threshold was further increased, the number of linkage regions genes within the top ten rose, reaching a maximum score of 6/10 at cutoff IU levels between 560 and 620. Scores of 6/10 between the 560 and 620 IU cutoffs were considered to be significantly higher than the background linkage region scores for the same IU cutoffs (p=0.028).  
      Since higher IU levels reflect increasing gene expression, the peak of SZ-linked region genes between the 560 and 620 IU cutoffs indicates the range of expression levels at which the noise of the system from in-specific differential gene expression has been filtered out. The remaining genes show disease-specific differential gene expression. Therefore, the overabundance or enrichment of top ranking genes that map to SZ linkage regions, seen at those cutoff levels, may provide the best candidate genes for DNA sequence analysis to search for gene and/or promoter, enhancer or splicing mutations.  
      At IU cutoffs over 620, the number of SZ-linkage region genes then fell back as the threshold was increased, dropping to a plateau of 2/10 at an IU cutoff of 720. The decreased representation of SZ-linked region genes in the top ten differentially expressed genes at IU cutoffs greater than 620 may be due to increasing representation of leukocyte-specific gene expression at these higher levels. This representation is likely due to, or reflective of, alterations in leukocyte expression of immune response mediator (IRS) and other genes, previously reported for SZ, and also due to the multigene expression patterns observed in the preliminary data for this study. Using this preliminary data, it was discovered that among the genes most significantly differentially expressed in leukocytes, between SZ and control subjects, there is a significant overrepresentation of genes from areas of reported linkage to SZ.  
     Methods  
      Autosomal genes were sorted by increasing two tailed t-test significance level of differential expression (p value). For the purposes of this example genes/ESTs were designated “expressed” if they had a GeneChip intensity of ≧100 intensity units (IU), and 1042 of the mapped, expressed genes were found to be differentially expressed (p&lt;0.05) between the SZ and healthy CS groups.  
      Mapped-gene/EST expression data were then filtered using increasing GeneChip intensity thresholds, and the ten top ranking genes were each scored as mapping either to a region of SZ linkage (1), or to another genome region (O). The ten top ranked gene/EST&#39;s scores were summed and recorded. When all autosomal mapped genes/ESTs were included in the analysis (zero intensity filter) 2/10 genes/ESTs fell within a region of linkage.  
      Genome mapping. Genes and ESTs represented as oligonucleotide probe-sets on the Affymetrix HU95A version 2 arrays, were mapped to their chromosomal sequence locations using the Ensemble Human Genome Browser (80%) and NCBI Human Genome Resource databases (20%). A total of 9774 genes and ESTs were mapped using these automated approaches, Genes without mapping data were excluded from the dataset.  
      A sample of genes and ESTs (n=81) that had not been mapped by the automated approach, were mapped manually. There was no significant difference in the proportion of linkage area genes, when the manual and automated mapping approaches were compared (p=0.689), indicating that the automated gene mapping approach was not biased in the genes that it mapped.  
     Results and Discussion  
      As illustrated in  FIG. 6 , a filter of increasing expression level stringency was applied in 20 IU increments, excluding genes for which less than two subject&#39;s IU values equaled or exceeded the IU threshold for that gene. Genes/ESTs that mapped to regions of linkage were assigned a score of 1. Genes/ESTs mapping to other areas of the genome were scored 0. The dataset was filtered with increasing stringency, using signal intensity cutoffs in 20 unit steps (i.e., ≧0, 20, 40, 60, . . . ). For each intensity cutoff, the number of genes/ESTs within the top 10 of all genes/ESTs, that map to regions of linkage were counted, and the y-axis values for the filled red circles each indicate the sum total of linked genes/ESTs within the top 10 genes/ESTs that were present, using the x-axis intensity cutoff level. The filled black circles indicate sum total of randomly occurring linkage areas within the top ten gene/ESTs. Thirty complete, independent sets of randomized mapping data were generated and used to determine the frequency of random gene mapping to a linkage region.  
      This reasoning was based on the hypothesis that IU levels reflected increasing gene expression. Therefore, the peak of SZ-linked region genes between the 560 and 620 IU cutoffs indicates the range of expression levels at which the noise of the system from in-specific differential gene expression has been filtered out, leaving genes that show disease-specific differential gene expression. Accordingly, the overabundance or enrichment of top ranking genes that map to SZ linkage regions, seen at those cutoff levels, may provide the best candidate genes for DNA sequence analysis to search for gene and/or promoter and/or enhancer mutations or alterations.  
      A recent genome scan meta-analysis (GSMA) was used to select linkage regions for this preliminary analysis of gene expression data. (Lewis et al. Am. J. Hum. Genet. 2003; 73:34-48). In this approach a rank-based meta-analysis was applied to autosomal data from 20 genome scans. Marker data was assigned to individual 30-cM bins and the bins were ranked by linkage scores, with weightings for sample sizes. Permutation testing was used to calculate the probabilities of the observed bin ranks, and 19 autosomal regions were identified where p&lt;0.05 for weighted and/or unweighted analyses. Accordingly, in one embodiment, genes/ESTs identified in the present invention that map to the regions identified in the Lewis study are considered as being potentially SZ susceptibility loci.  
      The results demonstrate that that thirty three percent of the genes and ESTs were mapped to regions where linkage has been reported in a genome scan meta-analysis of 20 genome scans (Lewis et al., Am. J. Hum. Genet. 73:34-48, 2003).  
      Prevalence of Significantly Differentially Expressed Genes is Enriched in Areas of Linkage to SZ. The total number of genes that map to SZ-linked areas were then compared with the total for genes that map to non SZ-linked areas of the genome. Interestingly, there was a 3.83 fold excess over expected values of significantly differentially expressed genes (p&lt;0.05) mapped within SZ-linkage areas, compared to the total number of genes/ESTs that map to areas of SZ linkage. This enrichment finding further suggests that some of these differentially expressed genes may be good candidates for being “disease or Susceptibility genes” for SZ.  
      Linkage Data is not a Prerequisite or Requirement for Practice of the Invented Method.  
      In many complex diseases, disorders and physical states, linkage data is not strong or reliable, or may not be available. One preferred embodiment of the present invention involves utilization of altered expression of surrogate tissue in a subject or subjects, for the identification of candidate sequences for testing by sequence analysis, without further selection based on whether genes/ESTs or nucleotide sequences lie at or near a region reported or considered to be linked to the disease, disorder or physical state being investigated.  
     Example 8B  
     Prostate Cancer  
      There is also substantial evidence of a significant hereditary component in susceptibility to—and of familial aggregation of—prostate cancer (PCa), with epidemiological studies having demonstrated a 2-3 fold increased risk of PCa amongst first-degree relatives of PCa patients (Whittemore et al, Am J Epidemiol. 1995, 141, 732-40). Although there are issues of heterogeneity, multiple studies have identified areas of linkage to the disease (Easton et al., The Prostate, 57: 261-269, 2003; Janer et al., The Prostate, 57: 309-319, 2003; Brown et al., Brit J. Cancer, 90: 510-514, 2004; Witte et al., The Prostate, 57: 298-308, 2003; Cunningham et al., The Prostate, 57:335-346, 2003; Verhage et al. Familial Cancer, 2: 57-67, 2003). Several of the linkage regions have been identified and confirmed in independent populations. Regions identified to date include 1p36, 17q11, 19 p13, 20q13 and Xq27-28. These results to date indicate the presence of multiple PCa susceptibility loci, and several individual genes within the regions have been identified as potential candidate PCa susceptibility alleles, these include RNA-SEL and ELAC2 (Carpten et al., Nat Genet, 30: 181-184, 2002; Tavtigian-S V., Nat Genet, 27:172-180, 2001).  
      The methods of the present invention were used to analyze expression data from men with PCa (n=11) and male control subjects (n=7). About 40% of the genes and expressed sequence tags (ESTs), represented on the HU95A version 2 GeneChip microarrays, used in this example were considered to be expressed (by the selected cutoff) in the leukocyte samples used, indicating that this accessible surrogate tissue is useful for the discovery and/or identification of candidate genes/ESTs by measurement of differential expression of genes/ESTs. About 599 genes were significantly differentially expressed between the PCa patient and control subject groups (p&lt;0.05).  
      Mapping to the human genome was performed as described above.  
     Results  
      Differentially Expressed Genes Map to Areas of PCa Linkage. When the differentially expressed genes were ranked by significance level and mapped to the human genome as above, 55% of the 20 most significant genes were mapped close to regions of published replication-confirmed linkage to PCa. In order to control for any potential issues of PCa-linked genome regions possibly being over represented on the microarray, and to investigate the number of PCa linkage region genes that would be expected to appear in the top 20 by chance alone, repeated randomizations of the data were performed, and these were found to consistently result in about 20% of the top 20 genes mapping within regions of linkage to prostate cancer.  
      This strongly suggests to that the present invention will be useful for the rational discovery and/or detection and/or assay of potential candidate genes for mutation screening.  
     Example 8C  
     Potential Candidate Genes or ESTs  
      Initial examination of pilot expression data and linkage regions has indicated a number of genes that are differentially expressed in PCa, and that map to regions of PCa linkage. Several are described below.  
      On candidate gene which was found to be significantly differentially expressed between PCa patients and healthy controls, and that maps to a region of linkage, is the potassium voltage-gated channel, shaker-related subfamily, beta member 2 (HKvbeta2.2) gene, which was mapped to 1p36.3 (within 6cM of the positive LOD score region). This gene also was found to be upregulated in PCa subject group (p=0.000041) (Gibbs et al., Am J Hum Genet, 64: 776-787, 1999). This gene is of additional interest because there is evidence of voltage-gated potassium ion channel protein overexpression in PCa specimens, and potassium channel blocking agents demonstrated growth inhibition in the LNCaP prostate tumor cell line (Abdul and Hoosein, Cancer Letters, 186: 99-105, 2002).  
      A second potassium channel gene that is significantly differentially expressed between PCa patients and healthy controls, and that maps to a region of linkage, is the Shaw type potassium voltage-gated channel Kv3.3 (KCNC3) gene. This gene was mapped to 19q13.3-q13.4, and was upregulated in PCa subject group (P=0.0017).  
      These findings indicate the utility of this invention for discovery, identification, detection, and evaluation of genes that are likely candidates for involvement in PCa susceptibility. Use of surrogate tissues and/or cells and/or organs (in PCa, peripheral blood leukocytes) permits of subject choice, and in the case of PCa, does not depend on the ability to acquire normal prostate or prostate tumor tissue, thus broadening the availability of samples by avoiding the requirement for a prostate biopsy.  
     Example 8D  
     Proposed Study for Identification of Candidate Genes in Schizophrenia  
      This proposed study is designed to test the feasibility of expression and linkage mapping as a method for discovering candidate genes within linkage regions, and to perform mutation analysis of the candidate genes. The longer term aims for this research are to extend this research to other psychiatric disorders and other diseases, disorders and physical states and all ethnicities.  
      Study Design. Blood leukocytes from twenty male and female SZ patients of non-Hispanic Caucasian ethnicity and twenty healthy control subjects between the ages of 2165 will be collected over the two year period of this study. Affymetrix GeneChip microarray (e.g., U133A) technology will be employed to measure global gene expression in the leukocyte samples, and significance testing will be conducted to identify genes differentially expressed between the two subject groups.  
      Genes and ESTs that are significantly differentially (p&lt;0.05) expressed between the patient and control groups will be finely mapped to their genomic locations. The alignment settings will be stringent, only matches that have greater that about 98% identity or less than or more than 98% identity will be considered. In addition, significantly differentially expressed genes and ESTs that map within or near flanking markers of linkage to SZ will be cataloged and sorted by patient/control differential expression significance or level. Genes that map between or near the two markers of regions of linkage that has been will be included. Particular focus may be on areas previously shown or suggested to be linked to SZ, may include eg. 1q21-22, 6p22-24m, 6q21-22, 8p21m 10p1-15, 13q32, 22q11-13, and may also include 1q23.3-q31.1, 2p12-q22.1, 3p25.3-p22.1, 5q23.2-q34, 11q22.3-24.1, 6pter-p22.3, 2q22.1-q23.3, 1p13.3-q23.3, 8p22-p21.1, 6q15-q23.2, 6p22.3-p21.1, 10pter-p14, 14pter-q13.1, 15q21.3-q26.1, 16 p13-q12.2, 17q21.33-q24.3, 18q22.1-qter, 20 p12.3-p11, 22pter-q12.3 (Lewis et al., Am J Hum Genet. 2003; 73(1):3448).  
      Candidate genes cataloged as described above that have altered expression between the patient and control groups and that may also be included based on other factors eg. known or predicted to be expressed in the brain, will be selected The candidate genes/ESTs or sequences, including 5′ and 3′ untranslated regions, controlling regions and all intron/exon boundaries will be sequenced in all patients and controls to determine mutations or sequence alterations.  
      Future studies such as evaluation using gene chips or other microarrays or other technologies, with more genes/ESTs or sequences (e.g., U133 plus 2.0 from Affymetrix), may also include the investigation of genes/ESTs or sequences that have altered expression or eg. are differentially regulated between subjects with and without, and between different psychiatric disorders such as bipolar disorder and major depression and other disease, disorders or physical states.  
     Example 9  
     Refinement of Analysis to Detect Genetic Alterations  
      The following methods can be used, (either individually, or in combinations of one or more additional methods), but are not a requirement for the practice of the invention. One or more of these refinements can be used in conjunction with the initial invention to facilitate identification genetic defects by evaluating RNA expression in “surrogate” tissue.  
      Refinement One. Employment of the present method preferentially selects evaluation of genes or ESTs or other sequences of interest that are physically located within, near, or in the region of an area of linkage to the disease, disorder or physical state of interest. Such selection increases the likelihood that sequencing of a candidate loci meeting this criteria will yield a mutation or other genetic defect or alteration that is related to the disease, disorder or physical state of interest.  
      Refinement Two. The present method employs expression level-based exclusion filtering criteria to remove potentially spurious and/or non-relevant RNA expression data from data sets, following identification of candidates as described above. This technique can be applied by utilizing lower and upper expression level cutoffs. This is relevant to the present invention since it may be difficult to identify candidates among very low level expressors. Therefore, by using a “surrogate” or non-directly related biological sample tissue, any observed differential expression may be a product of non-physiological expression alterations. This rationale also applies in the case of high expressors, again because of the use of “surrogate” or non-directly related biological sample source. In this case, high expressors can be excluded as being of physiological importance in that sample or subject, unless, there is evidence the genes/ESTs/sequences under investigation have physiological relevance to the sample.  
      Refinement Three. The present method employs statistical testing to determine the significance of the differential expression between experimental groups being tested, i.e. “disease” and “healthy” or different physical state groups. This enables sorting or ranking of the genes/ESTs/sequences under investigation by the significance of their differential expression. Their relative significance can then be a factor in the selection of candidate genes/ESTs/sequences that are further selected for sequencing in search of genetic alterations or defects.  
      Refinement Four. A fourth refinement is the use of the size and/or degree of expression difference between experimental groups being tested, i.e., between “disease” and “healthy” or physical state groups. The genes/ESTs/sequences under investigation can then be sorted and/or ranked by the size and/or degree of their differential expression, and their relative expression difference size will then be a factor in the selection of candidate genes/ESTs/sequences that are further selected for sequencing in search of genetic alterations or defects.  
      Refinement Five. The present invention also exploits expression information relating to the disease and/or condition and/or state under investigation. Information from studies or databases or other sources can be utilized as a method for filtering genes/ESTs/sequences to aid in the choice of candidates for further investigation by sequencing or other methods. Utilization of disease specific, tissue specific, or other specific expression information could also be a factor in deciding whether to exclude or include genes/ESTs/sequences from further analysis.  
      Refinement Six. Another refinement concerns use of expression information relating to organs, tissues, cells that are related to the disease or physical state under investigation. Information from studies or databases or other sources can be utilized as a method for filtering genes/ESTs/sequences to facilitate the selection of candidates for further investigation by sequencing or other methods.  
      This additional method is best applied by using it as a factor in the selection of candidates for further investigation, i.e., assessing whether genes/ESTs/sequences under consideration are expressed or differentially expressed or have altered expression, in tissues associated with to the disease or physical state under investigation. Thus, for example, for schizophrenia, preference or priority for further investigation may be given to genes/ESTs/sequences that are expressed in the brain or central nervous system. Conversely these type of criteria could also be utilized in exclusion genes/ESTs/sequences from further analysis.  
      Refinement Seven. This invention exploits information concerning gene, loci, sequence and expression information relating to the disease, disorder or physical state under investigation. Information from studies or databases or other sources can be utilized as a method for selecting genes/ESTs/sequences to measure/assay based on expression levels in order to assess samples for the potential presence of mutated and/or altered genes and/or sequences. For any disease, disorder or physical state under investigation, information from studies or databases or other sources is utilized to generate listings of genes/ESTs/sequences as potential candidates. For example, where a previous study has named a gene as being of interest or shown association with, or has suggested biological or genetic expression or activity or function, in a disease, disorder or physical state, there is a rationale for its consideration as a candidate disease gene.  
      The present invention is not to be limited in scope by the specific embodiments described herein. Indeed, various modifications of the invention in addition to those described herein will become apparent to those skilled in the art from the foregoing description and the accompanying figures. Such modifications are intended to fall within the scope of the appended claims.  
      It is further to be understood that all values are approximate, and are provided for description.  
      Patents, patent applications, publications, product descriptions, and protocols are cited throughout this application, the disclosures of which are incorporated herein by reference in their entireties for all purposes.