Patent Publication Number: US-2018046754-A1

Title: Normalization methods for measuring gene copy number and expression

Description:
FIELD OF THE INVENTION 
     The present invention relates to method(s) for measuring gene copy number and gene expression, quantitative PCR, qRT-PCR, normal individuals, medical conditions including the patients with cancer, ovarian cancer, ovarian serous adenocarcinoma, cancer diagnosis, cancer detection, therapy monitoring and laboratory diagnostics. 
     BACKGROUND OF THE INVENTION 
     The gene copy number (also gene “copy number variants” or CNV) is the number of copies of a particular gene in the genotype of an individual. In the human genome, DNA encodes more than 25,000 protein coding genes and many thousands of non-protein coding genes. It was generally thought that genes in somatic cells were almost always present in two copies in a genome. However, recent discoveries have revealed that larger numbers of the segments of DNA could be observed. The size of such segments ranges from hundreds to millions of DNA bases, providing variation in DNA segment/gene copy-number. Such differences in the CNV of the individual genomes occurs in normal body cells, contributing to the organism&#39;s uniqueness. However, these DNA amount changes also influence most traits including susceptibility to disease. CNV can encompass individual genes and their clusters leading to dosage imbalances. For example, genes that were thought to always occur in two copies per genome have now been found to sometimes be present in one, three, or more than three copies. In various medical conditions and disease progression states, some DNA loci containing key regulatory genes are missing. 
     Gene or DNA copy number (CN) is usually measured by an average number of DNA copies per genome per cell in a biological sample. Gene copy number variation (CNV) is observed in normal tissue samples and is amplified in certain diseases, such as cancers. It has previously been demonstrated that CNV of a given gene directly affects its expression. The exact relationship between the CNV and the gene expression values is poorly studied but it is thought to be a nonlinear relationship which depends on cell, tissue, organism and medical conditions. The accurate and reproducible detection of CN and CNV of a given genome locus (or loci) and an establishment of their quantitative interconnection with the variation of expression of a gene belonging to a given CNV locus (or loci) is a great challenge. A practical solution of this problem is urgently needed for optimization of healthcare strategies, evaluation of the status of normal individuals and for diagnosis, prognosis and prediction for patients with medical conditions. 
     qPCR-based assays are considered as “gold standards” for detecting a variety of medical conditions attributed to gene expression changes and are broadly used in common clinical practice. Gene expression level in the cells and/or tissue samples is usually ranged within 5-6 orders of magnitude and a detection of the variation of such characteristics is provided by qPCR-based techniques, often with high accuracy. However qPCR-based assay interpretation is majorly dependent on measurement of cycle threshold (CT) values of the target gene(s) relative to CT values of reference/normalizing gene(s) (e.g. ACT B, GAPDH etc.). This condition might be a limitation in the context of cell or tissue specification and of bio-medical or environmental conditions, due to a systematic or random error variation that could occur in the reference/normalizing gene(s). In particular, some of the reference/normalizing gene(s) can also vary in a correlated manner with expression levels of the gene(s) of interest in a given cell/tissue sample. For example, GAPDH, commonly used as a reference gene, is considered to be an oncogene in breast cancer as its expression level is highly correlated with cancer progression level. Therefore, this gene cannot be used as an invariant reference for breast cancer assays. The variation in expression levels of the reference/normalizing gene(s) could also be prone to non-specific and poorly controlled noise, due to the heterogeneous sample cell composition. Thus, in many cases conventional reference/normalizing gene(s) might not be usable as “universal” and “independent” controls providing robust, unbiased and accurate measurements of the expression of a given gene of interest estimated via CT value analysis calculations for a qPCR assay. An identification of adequate reference/normalizing gene(s) for the accurate, robust and reliable detection of the DNA copy number variation (CNV) of a given gene locus using qPCR-based assays appears to be more challenging. Firstly, the dynamical range of CNV detection is limited to a few delta-delta CT-values, which is a less accurate and more noise-prone measurement procedure than that of gene expression. Secondly, the actual measurement in a cell/tissue sample is defined by delta-delta CT-values, averaged across many cells of a biological sample. CNV of the “control” genes across a single sample can be observed even in normal tissue samples, and is much more amplified in some pathological cases. Thirdly, in certain diseases, such as serous ovarian carcinoma, CNV of a given gene might directly affect the gene expression. The exact relationship between the CNV and the expression values is poorly understood and might be non-linear. Present methods for measuring gene CN and expression have been designed ignoring these facts. Therefore, gene CN and expression values obtained with any existing measurement method are affected by the unobserved CNV. Therefore, in such cases the CNV of the reference gene set also affects the observed expression values of any other gene measured in a given assay. Thus, the problem of indefinite CNV may invalidate any gene expression measurement. In many situations, such as those indicated above, more accurate, unbiased and robust reference/normalizing gene(s) should be identified, and appropriate primers should be optimized for use in detecting gene expression (mRNA/ncRNA) and CN (DNA) level. 
     SUMMARY OF THE INVENTION 
     Some embodiments relate to a method for determining a quantitative measure of a target gene in a biological sample from a subject, the method comprising:
         conducting an assay to measure respective quantities of the target gene and one or more reference genes or loci; and   normalizing the quantity of the target gene using the quantity or quantities of the one or more reference genes or loci, or a normalization function thereof;   wherein the one or more reference genes or loci are copy number-invariant genes or loci.       

     Other embodiments relate to a kit for obtaining reference gene measurements in one or more biological samples, the kit comprising oligonucleotide primers capable of binding to and/or amplifying at least a portion of the nucleic acid sequence, and/or cDNA derived therefrom, of at least one gene selected from the group consisting of: XRCC5; AUTS2; EIF5; PARN; YEATS2; and FHL2. 
     According to a preferred embodiment of the kit, the primer sequences are selected from or derived from oligonucleotide sequences identified in Table 6 as SEQ ID Nos: 1-24. 
     According to a preferred embodiment of the kit, the primers are capable of binding to and/or amplifying at least a portion of the nucleic acid sequence, and/or cDNA derived therefrom, of at least one locus selected from Table 1, Table 2, Table 3, Table 4, Table 5, Table 8, Table 9, Table 10, Table 11, Table 13 or Table 14. 
     Further embodiments relate to a computer program or a computer device comprising a computer program which is capable of implementing the method according to any aspect of the present invention. 
     Further embodiments relate to a computer-implemented method for identifying reference genes and/or loci for relative quantitation of a target gene or locus, the method comprising:
         receiving, by a reference gene/locus identification component, training data indicative of: copy numbers of a plurality of genomic segments in a plurality of pathological and/or non-pathological biological samples; corresponding RNA expression levels of genes/loci within or overlapping with said segments; and ranges of genomic coordinates of said segments;   assigning respective ones of the plurality of genomic segments to one of a plurality of non-overlapping genomic partitions;   determining, by the reference gene/locus identification component from the copy numbers of genomic segments in respective partitions, invariant partitions which are not subject to copy number variation; and   identifying, by the reference gene/locus identification component using RNA expression levels of genes/loci in the invariant partitions, a set of reference genes/loci comprising genes/loci which do not substantially vary in expression level across the plurality of biological samples.       

     Yet further embodiments relate to a computer-implemented method for identifying reference genes/loci for relative quantitation of a target gene/locus, the method comprising:
         receiving, by a reference gene/locus identification component, training data indicative of: copy numbers of a plurality of genomic segments in a plurality of pathological and/or non-pathological biological samples and ranges of genomic coordinates of said segments;   assigning respective ones of the plurality of genomic segments to one of a plurality of non-overlapping genomic partitions;   determining, by the reference gene/locus identification component from the copy numbers of genomic segments in respective partitions, invariant partitions which are not subject to copy number variation.       

     Yet further embodiments relate to a method for measuring target gene(s) DNA copy number in one or more samples, the method comprising:
         identifying one or more reference loci by a method according to any of the above embodiments;   for each sample, obtaining copy number measurements for the one or more reference loci;   for each reference locus, obtaining a numeric integrative measure of its DNA copy number values across the training data samples as a normalization factor;   for each of the one or more samples, obtaining the copy number value of the target locus (or loci); and   for each DNA copy number value of the target locus (or loci), obtaining its normalized copy number value by applying a normalization procedure using the normalization factor and a normalization function.       

     Further embodiments relate to a system for identifying reference genes and/or loci for relative quantitation of a target gene or locus, the system comprising:
         a reference gene/locus identification component which is configured to:   receive training data indicative of: copy numbers of a plurality of genomic segments in a plurality of pathological and/or non-pathological biological samples; corresponding RNA expression levels of genes/loci within or overlapping with said segments; and ranges of genomic coordinates of said segments;   assign respective ones of the plurality of genomic segments to one of a plurality of non-overlapping genomic partitions;   determine, from the copy numbers of genomic segments in respective partitions, invariant partitions which are not subject to copy number variation; and   identify, using RNA expression levels of genes/loci in the invariant partitions, a set of reference genes/loci comprising genes/loci which do not substantially vary in expression level across the plurality of biological samples.       

     Yet further embodiments relate to a system for identifying reference genes/loci for relative quantitation of a target gene/locus, the system comprising:
         a reference gene/locus identification component which is configured to:   receive training data indicative of: copy numbers of a plurality of genomic segments in a plurality of pathological and/or non-pathological biological samples and ranges of genomic coordinates of said segments;   assign respective ones of the plurality of genomic segments to one of a plurality of non-overlapping genomic partitions;   determine, from the copy numbers of genomic segments in respective partitions, invariant partitions which are not subject to copy number variation.       

     Other embodiments relate to a non-transitory computer readable medium having program instructions stored thereon for causing at least one processor to carry out the method according to any of the above embodiments. 
     Embodiments of the present disclosure relate to a novel method for obtaining accurate CN and gene expression measures of a given gene of a given subject via normalizing the measured values onto CN of the proposed DNA sequences (rtPCR/qPCR) primers associated with one (or more) of the obtained reference genes selected by a reference gene identification method which works at the genome level across populations of individuals and diverse medical conditions. 
     In certain embodiments, specified DNA sequences of a reference gene set, along with loci coordinates of the respective primers, might be optimized for a given patho-biological context and medical conditions. The practical efficacy/power of embodiments of the method is demonstrated using epithelial ovarian cancer (EOC) samples. Embodiments propose a reference gene set previously never used as a reference or normalization control in qPCR-based assays. This set is proposed for use in detection of expression and DNA copy number variation in ovarian serous adenocarcinoma samples. Embodiments also provide a computational method allowing one to select “reference and normalization” genes for any sample set, sharing specific biological or pathological characteristics, such as tissue of origin or/and medical condition. 
     Some embodiments relate to an in vitro method for obtaining information on the number of DNA copies (CN) of a given locus of interest in a biological sample, the method comprising: 
     i) obtaining the CN value of the locus of interest in the biological sample; 
     ii) obtaining the CN value or values of one or more CN-invariant locus reference(s) (CNILR) in the biological sample, wherein the CNILR is defined as a which is locally CN-invariant, or as a locus with a minimal coefficient of variation value of its CN values across said group; 
     iii) obtaining the CN value or values of or one or more CN-invariant survival-insignificant locus reference(s) (CNISILR), wherein the CNISILR being defined as a CNILR, whose CN value, or any expression value of the genes within the locus, cannot define more than one subgroup of said group, based on survival prediction analysis; and 
     iv) normalizing the CN value of the locus of interest by the CN value of said one or more CNISILRs if defined, otherwise normalizing the CN value of the locus of interest by the CN value of said one or more CNILRs. 
     In a preferred embodiment, said one or more CNILRs in the biological sample is/are determined by: 
     i) providing a representative reference data set containing measurements of genome-wide CN variation with respect to a group of samples; 
     ii) identifying a set of loci with the lowest variation across the reference data set as the reference loci; 
     iii) ranking the reference loci by their median CN values across the reference data set; and 
     iv) selecting one locus or a set of loci with the highest median CN value(s) as the CNILR(s). 
     In another preferred embodiment, said one or more CNISILRs in the biological sample is/are determined by: 
     i) providing a representative reference data set containing measurements of genome-wide CN variation with respect to a group of samples; 
     ii) identifying a set of loci with the lowest variation across the reference data set as the reference loci; 
     iii) identifying a subset of loci, whose functions and/or transcriptional activity are not statistically associated in the reference data set, as loci with no significant statistical association; 
     iv) ranking the loci with no significant statistical association by the coefficients of variation of the expression values of the transcripts originating in these loci across the reference data set; and 
     v) selecting one locus or a set of loci with the lowest coefficient(s) of variation of the CN values as the CNISILRs. 
     The normalization may be conducted by normalizing the CN value of the locus of interest by the CN value of the CNISILRs. Alternatively, or in addition, normalization is conducted by normalizing the CN values of the locus of interest by the median CN values of more than one CNISILRs. Normalization may also be conducted by normalizing the CN value of the locus of interest by the CN value of one CNILR or by the median CNNILRs. 
     According to a preferred embodiment, said one or more CNILRs or CNISILRs is one or more loci from the group consisting of: XRCC5; AUTS2; EIF5; PARN; YEATS2; and FHL2. 
     More particularly, said one or more CNILRs or CNISILRs is/are selected from the loci identified in Table 1, Table 2, Table 3, Table 4, Table 5, Table 8, Table 9, Table 10, Table 11, Table 13 or Table 14. 
     According to a preferred embodiment, said one or more CNILRs or CNISILRs is/are selected if the coefficient of variation is less than a computationally or empirically predetermined threshold is equal to 0.05. 
     Some embodiments relate to an in vitro method for determining the CN of a target gene in a biological sample, the method comprising:
         1. obtaining the CN measurement of one or more CN-invariant genes   2. obtaining the CN measurement of the target gene   3. determining the CN value of the target gene from the ratio of the first two measurements.       

     Other embodiments relate to a method for determining the set of CN-invariant loci in a given set of samples, the method comprising:
         1. obtaining the set of samples as the training set   2. for the samples in the training set, obtaining the genome-wide segmentation by uniform CN values   3. for each said CN segment determining its CN value in each sample   4. from the CN of the segments across all the samples, calculating the upper and lower CN thresholds that would mark a segment as amplified or deleted if its CN is above the upper or below the lower threshold, respectively   5. using the upper and the lower CN thresholds, identify the CN-aberrated (i.e. amplified or deleted) segments across all the samples   6. partitioning the genome in non-overlapping intervals without gaps (e.g. cytobands)   7. define individual loci in the genomic coordinates (e.g. genomic coordinates of genes)   8. for each genomic partition and each locus, identifying the number CN-aberrated segments overlapping with its genomic coordinates   9. identifying the partitions and the loci containing no CN-aberrated segments as CN-free loci and partitions, respectively   10. identifying such said CN-free loci that are located within the genomic coordinates of the said CN-free partitions as CN-invariant loci.       

     Further embodiments relate to an in vitro method for determining the expression of a target gene in a biological sample, the method comprising:
         1. obtaining the gene expression measurement of one or more CN- and expression-invariant genes   2. obtaining the gene expression measurement of the target gene   3. determining the gene expression value of the target gene from the ratio of the first two measurements.       

     The CN value of the locus of interest and/or of said reference locus or loci in the biological sample may be determined as a gene expression value originating from a transcript of said locus. 
     In a preferred embodiment of any aspect of the present invention, the sample is obtained from cells or tissues from cancer patients or cell cultures derived from cancer patients. 
     The cancer patients may have a cancer type or subtype selected from ovarian cancer, breast invasive carcinomas, head and neck squamous cell carcinoma, lung adenocarcinoma, lung squamous cell carcinoma, prostate adenocarcinoma, colon adenocarcinoma, stomach adenocarcinoma, hepatocellular carcinoma, or cervical squamous cell carcinoma. 
     In a preferred embodiment, the sample is obtained from cells or tissues obtained from myocardial infarction patients or cell cultures derived from myocardial infarction patients. 
     Yet further embodiments relate to a method for determining the set of CN- and expression-invariant loci that can be used as a references for target gene expression measurements, the method comprising:
         1. obtaining the set of CN-invariant loci for a given training set of samples   2. for each said CN-invariant locus, measuring across the samples the expression of the gene (or genes) located within the genomic coordinates of the locus   3. for each said CN-invariant locus, identifying a single gene with the highest measure of variation (e.g. coefficient of variation) of expression across the samples as the representative gene   4. from the list of the loci—representative gene pairs selecting such whose measure of variation is smaller than a given threshold (e.g. coefficient of variation less than 0.05) as the set of CN-invariant loci that can be used as references for target gene expression measurements       

     Yet further embodiments relate to a method for determining the optimal range of gene expression values that can be measured using the CN- and expression-invariant genes as references. 
     Yet further embodiments relate to CN- and gene expression measurements in ovarian cancer samples. 
     The present invention is further defined in accordance with the claims appended hereto. 
    
    
     
       DETAILED DESCRIPTION 
       The present invention will now be further described by way of example and with reference to the Figures which show: 
         FIG. 1 . The majority of genes in HG-SOC samples obtained from patients at any stage of the disease contain CNVs. The disease stages are denoted with Roman numerals (I-IV). Fallopian tube samples (denoted as “F”) obtained from HG-SOC-affected patients were used as a control; 
         FIG. 2 . CNV in chromosome 1 of HG-SOC samples (stages I-IV) and fallopian tubes (“F”) per megabase of the genomic distance (X axis). The Y axis shows the fraction of a) samples with CNV in a given megabase (black circles) and b) genes with CNV in a given megabase (grey circles). The arrows indicate the CNV-invariant regions that are used as sources of CNV-invariant genes; 
         FIG. 3 . Actin family genes reveal CNV in HG-SOC patients; 
         FIG. 4 . An embodiment of an algorithm to choose CNV-invariant genes; 
         FIG. 5 . An embodiment of an algorithm to choose the gene expression range optimal for using the CNV-invariant genes as references for gene expression measurements; 
         FIG. 6 . Primer melting curves for exemplary reference genes; 
         FIG. 7 . Reproducibility of the qPCR signal measuring the reference genes CN values in biological replicas; 
         FIG. 8 . Reproducibility of the qPCR signal measuring the reference genes expression values across biological replicas; 
         FIG. 9 . The CT values variation obtained from the qPCR of the reference genes genomic DNA; 
         FIG. 10 . The CT values variation obtained from the qPCR of the reference genes expression; 
         FIG. 11 . The copy number variation, detected with CGH microarrays, within the genes most commonly used as references for qRT-PCR measurements; 
         FIG. 12 . The qPCR measurements of MECOM DNA copy number across ovarian serous adenocarcinoma tumor (T) and normal ovarian epithelium (N) control samples. The expected MECOM CN was obtained by normalization of its CT values by the median values of one of the normalziation reference genes. ACTB was selected as the traditional normalization reference. AUTS2, YEATS2, EIF5, XRCC5, and PARN were selected to represent the normalization references obtained by the proposed method. A) the difference between the tumor and the control median MECOM CN (the Wilcoxon test P-values are given); B-C) coefficient of variation of the MECOM CN across the tumor (B) and the control (C) samples; D-G) the estimated MECOM CN in the individual tumor (T) and control (N) samples; 
         FIG. 13 . Application of the present candidate loci, instead of traditional control loci (ACTB, TBP, and GAPDH), can improve an existing DNA-based clinical diagnostic assay Therascreen EGFR EGQ PCR Kit (Qiagen) measuring the DNA copy number of EGFR gene. Genes from our panel designed specifically for ovarian cancer, can improve the coefficient of variation of the EGFR DNA copy number in 8 out of 10 most common cancers, covering 50% of all cancer patients. Two reference loci providing the lowest and the highest variation of the EGFR CN measurements across the given samples are marked with the dark grey and the light grey colours, respectively; 
         FIG. 14 . Application of the candidate reference loci can improve an existing DNA-based assay Human Breast Cancer Copy Number PCR Array (Qiagen) measuring the DNA copy number of 23 loci reported to vary in breast cancer tumors. Across the breast invasive carcinoma (A), for 22 out of the 23 loci the lowest variation is obtained with the proposed candidate reference loci used as normalization controls, but not with the traditional control loci (ACTB, TBP, and GAPDH). Across the lung adenocarcinoma samples (B), for all 23 indicator loci of the assay the median variation of the markers obtained with our control loci was lower than the lowest variation obtained using any of the traditional control loci. Each cell of the matrix displayed as a rectangular heat map (in each panel) represents expression a gene of interest (in rows) normalized by a given reference locus (in columns). The colour intensity in each cell represents the expression value (growing from white to black); 
         FIG. 15 . Application of the present candidate loci can improve an existing DNA-based assay Human Breast Cancer Copy Number PCR Array (Qiagen) measuring the DNA copy number of 23 loci reported to vary in the breast cancer tumors. Two reference loci providing the lowest and the highest variation of the median CN measurements across the given 23 loci of interest, are marked with the dark grey and the light grey colours, respectively; 
         FIG. 16 . Application of the present candidate loci can improve the Human Breast Cancer Copy Number PCR Array (Qiagen) applied to analysis of head and neck squamous cell carcinoma (A) and lung squamous cell carcinoma (B). Each cell of the matrix displayed as a rectangular heat map (in each panel) represents expression a gene of interest (in rows) normalized by a given reference locus (in columns). The colour intensity in each cell represents the expression value (growing from white to black); 
         FIG. 17 . Application of the present candidate loci can improve the Human Breast Cancer Copy Number PCR Array (Qiagen) applied to analysis of ovarian serous adenocarcinoma (A) and colon adenocarcinoma (B) Each cell of the matrix displayed as a rectangular heat map (in each panel) represents expression a gene of interest (in rows) normalized by a given reference locus (in columns). The colour intensity in each cell represents the expression value (growing from white to black); 
         FIG. 18 . Application of the present candidate loci can improve the Human Breast Cancer Copy Number PCR Array (Qiagen) applied to analysis of prostate adenocarcinoma (A) liver hepatocellular carcinoma (B). Each cell of the matrix displayed as a rectangular heat map (in each panel) represents expression a gene of interest (in rows) normalized by a given reference locus (in columns). The colour intensity in each cell represents the expression value (growing from white to black); 
         FIG. 19 . Application of the present candidate loci can improve the Human Breast Cancer Copy Number PCR Array (Qiagen) applied to analysis of stomach adenocarcinoma (A) cervical squamous cell carcionma (B). Each cell of the matrix displayed as a rectangular heat map (in each panel) represents expression a gene of interest (in rows) normalized by a given reference locus (in columns). The colour intensity in each cell represents the expression value (growing from white to black); 
         FIG. 20 . The proposed method identified candidate normalization controls for DNA copy number measurements in the top 10 cancers. For each cancer a specific and a common set of loci are found and displayed as a Venn diagram; and 
         FIG. 21 . An embodiment of the presently disclosed method identified candidate normalization controls for DNA copy number measurements in the non-cancerous samples from three cohorts: a) genomes of 1000 healthy humans, b) genomes of the blood cells collected as controls. Displayed as a Venn diagram. 
     
    
    
     DEFINITIONS 
     Biological Terms 
     For convenience, certain terms employed in the specification and examples are collected here. 
     The term “aptamer” is herein defined to be oligonucleotide acid or peptide molecule that binds to a specific target molecule. In particular, an aptamer used in the present invention may be generated using different technologies known in the art which include but is not limited to systematic evolution of ligands by exponential enrichment (SELEX) and the like. 
     The term “comprising” is herein defined to be that where the various components, ingredients, or steps, can be conjointly employed in practicing the present invention. Accordingly, the term “comprising” encompasses the more restrictive terms “consisting essentially of” and “consisting of.” With the term “consisting essentially of” it is understood that the method according to any aspect of the present invention “substantially” comprises the indicated step as an “essential” element. Additional steps may be included. 
     The term “difference” between two groups of patients is herein defined to be the statistical significance (p-value) of a partitioning of the patients within the two groups. Thus, achieving a “maximum difference” means finding a partition of maximal statistical significance (i.e. minimal p-value). 
     The term “label” or “label containing moiety” refers to a moiety capable of detection, such as a radioactive isotope or group containing same and non-isotopic labels, such as enzymes, biotin, avidin, streptavidin, digoxygenin, luminescent agents, dyes, haptens, and the like. Luminescent agents, depending upon the source of exciting energy, can be classified as radio luminescent, chemiluminescent, bio luminescent, and photo luminescent (including fluorescent and phosphorescent). A probe described herein can be bound, for example, chemically bound to label-containing moieties or can be suitable to be so bound. The probe can be directly or indirectly labelled. 
     The term “locus” is herein defined to be a specific location of a gene or DNA sequence on a chromosome. A variant of the DNA sequence at a given locus is called an allele. 
     The term “copy number (CN) value” or “DNA copy number value” is herein defined to refer to the number of copies of at least one DNA segment (locus) in the genome. The genome comprises DNA segments that may range from a small segment, the size of a single base pair to a large chromosome segment covering more than one gene. This number may be used to measure DNA structural variations, such as insertions, deletions and inversions occurring in a given genomic segment in a cell or a group of cells. In particular, the CN value may be determined in a cell or a group of cells by several methods known in the art including but not limited to comparative genomic hybridization (CGH) microarray, qPCR, electrophoretic separation and the like. CN value may be used as a measure of the copy number of a given DNA segment in a genome. In a single cell, the CN value may be defined by discrete values (0, 1, 2, 3 etc.). In a group of cells it may be a continuous variable, for example, a measure of DNA fragment CN ranging around 2 plus/minus increment d (theoretically or empirically defined variations). This number may be larger than 2+d or smaller than 2-d in the cells with a gain or loss of the nucleotides in a given locus, respectively. 
     With respect to associations between disease and CN value, a level of variation (deviation) in a DNA segment CN might be important. A level of positive or negative increment of the CN from normal dynamical range in a DNA sample of a given cell group or a single cell may be called CN variation. 
     The term “sample” is herein defined to include but is not limited to be blood, sputum, saliva, mucosal scraping, tissue biopsy and the like. The sample may be an isolated cell sample which may refer to a single cell, multiple cells, more than one type of cell, cells from tissues, cells from organs and/or cells from tumors. 
     A person skilled in the art will appreciate that the present invention may be practiced without undue experimentation according to the method given herein. The methods, techniques and chemicals are as described in the references given or from protocols in standard biotechnology and molecular biology text books. 
     The method according to any aspect of the present invention may be in vitro, or in vivo. In particular, the method may be in vitro, where the steps are carried out on a sample isolated from the subject. The sample may be taken from a subject by any method known in the art. By way of non-limiting example, ovarian tumor material may be extracted from ovaries, fallopian tubes, uterus, vagina and the like. Metastatic tumor samples may be extracted from the peritoneal cavity, other body organs, tissues and the like. Cancer cells may be extracted from non-limiting examples such as biological fluids, which include but are not limited to peritoneal liquid, blood, lymph, urine, products of body secretion and the like. 
     The term “genomic object” here defines a physical element of a given genome. Examples of a genomic object include (but are not limited to) a chromosome, a chromosomal arm, a plasmid. 
     The term “locally CN-invariant gene/locus” here defines a gene/locus with the number of copies, averaged across the span of the genomic coordinates of said gene/locus, staying unchanged under any extension of the locus&#39; span within the entire genomic object. 
     The term “CN-invariant genes/loci in pathological samples”, or pathologically CN-invariant, here defines the genes/loci with average two copies per genome in pathological samples. The pathological samples can be represented by HG-SOC samples. A set of such genes/loci is listed in Table 1. 
     The term “CN-invariant genes/loci in normal tissues”, or biologically CN-invariant, here defines the genes/loci with average two copies per genome in tissue samples obtained from healthy humans. These samples can be represented by the ones collected in the Thousand Genomes project, for example. A set of such genes/loci is listed in Table 2. 
     The term CN-invariant genes/loci in human genome here defines the genes/loci being CN-invariant in both pathological and normal tissue samples. A set of such genes/loci is listed in Table 3. 
     The terms ‘invariant’ and ‘lowest variance’ here are used interchangeably for any data (including, but not limited to gene expression and copy number measurements), where variation across sample groups is not detected. 
     The terms ‘gene’ and ‘locus’ may be used interchangeably in the cases when the gene expression measurements are uncertain or irrelevant, for example when it is desired to quantify copy number but not gene expression. 
     The term genomic partition here defines a locus that includes the genomic coordinates of more than one gene. 
     The term cytoband here defines a genomic region that can be revealed by a standard cytogenetic staining (such as Giemsa staining). 
     The term human reference genome here defines the sequence annotated as the reference by the Genome Reference Consortium [Church D M, et al.,  PLoS Biology  9: 1001091 (2011)]. 
     Statistical Methods and Terms 
     The term “group of biological samples” is here defined as a collection of samples sharing one or more common biological or clinical property. Examples of such properties include (but are not limited to) tissue type, type of cells, source organism, the age of source organism, conditions of cellular growth, environmental conditions, treatment type. 
     The term normalization function here defines a function taking two arguments (the target and the reference), and returning one value. The function returns the scaling of the target in the units of the reference. The reference may be a single value or a set of values. An example of a normalization function is the ratio of the target value to the reference value. Standard score is an example of a normalization function, where the target is a single value, and the reference is a set: the standard score returns a scaling which is the ratio of the difference between the target value and the mean reference value to the standard deviation of the reference values. 
     The term normalization here defines a procedure of adjusting the values of the target measurement(s) by the values of the reference measurement(s), referred to as the normalization factor(s), using a normalization function. Typically, the normalization factor is the scaling returned by the normalization function. 
     The term reference gene here defines a gene that can be used as a normalization reference to obtain measurements of the target gene that would increase the measurements&#39; accuracy upon the normalization. 
     The term reference locus (plural—loci), also referred to as locus reference, here defines the genomic coordinate range that can be used as a normalization reference(s) for measurements of the target locus or gene that would increase the measurements&#39; accuracy upon normalization. 
     The term CN-invariant locus reference, also referred to as CNILR, in a given biological sample is here defined as a locus, which is locally CN-invariant; or in a biological sample representing a given group of biological samples the term CN-invariant locus reference is here defined as a locus with a minimal coefficient of variation value of its CN values across said group. 
     The term CN-invariant survival-insignificant locus reference(s) (CNISILR) in a biological sample representing a given group of biological samples, is defined as a CNILR, whose CN value, or any expression value of the genes within the locus, cannot define more than one subgroup of said group, based on survival prediction analysis. 
     The term numeric integrative measure here defines a function that takes a set of numeric values as an input and returns a single numeric value as an output. Examples of integrative measures are: mean, median, variance, maximum values. 
     The term robust measure is here defined as a measure, whose value does not significantly change if outliers are added to the measured data. Robustness of a measure may be defined for a specific measure compared to alternative measures of the same data (e.g. median vs. mean value estimation), or for a class of measures, compared to other classes of measures (e.g. a gene expression value measure with qPCR versus a gene expression microarray). 
     The term disease status information is here defined as a qualitative or quantitative variable defined for a patient (or a healthy subject) respective to a given disease, e.g. diagnosis, survival status (living or deceased) over a fixed time period, risk group, type of response to therapy, time after first disease recurrence. The particular value of a disease status information variable is here defined as the disease status. 
     The term disease status-significant genes is here defined as such genes that can stratify a cohort of patients into two or more groups by their given disease status with a given degree of statistical significance. 
     EXAMPLES 
     Example 1 
     Most of the genes in the genomes of EOC tumors (TCGA) are affected by CNV ( FIG. 1 ). For example, the CNV distribution across in Chromosome 1 ( FIG. 2 ) indicates that unlike the normal tissue control (fallopian tubes), EOC tumors at any stage of the disease include cells whose genomes carry numerous regions with CNV. Every chromosome and almost every tumor is affected. 
     The genomic regions unaffected by CNV typically spanned for a few megabases. The 851 cytobands containing no CNV, were selected as CN-invariant. The loci (obtained as the genomic coordinates of the longest transcription variants of the respective genes in the RefSeq database) affected by CNV were discarded, and 2841 unaffected genes were selected for further analysis. Among these genes, only 246 located in the CN-invariant cytobands (listed in Table 1). Such genes were considered CN-invariant. These loci and genes could serve as references for CNV measurement in EOC tumor samples. 
     To find such CN-invariant genes, which could be used as reference genes for both CNV and gene expression measurements, their median expression value and variance had to be assessed. For 157 of these loci (listed in Tables 2 and 3) Affymetrix U133A probes measured the expression of genes located in their genomic coordinates. These genes were considered CN-invariant and were tested for their expression median magnitude and variance across two cohorts of EOC tumors (TCGA and GSE9899). 
     As an additional criterion of robustness, the gene expression was tested for the significance of their expression values for the survival of the patients, using 1DDg method [Motakis E, et al.,  IEEE Eng Med Biol Mag  28: 58-66 (2009)]. Potentially, the CN and expression of survival-significant genes might change depending on the subgroup of the patients or treatment options, as the tumors expressing such genes might be subjects of selection. For the TOGA data set 92 genes (whose expression was measured by 121 probesets) satisfied this criterion, while in the GSE9899 data the number of such genes was 82 (with 117 corresponding probesets). Among them, 48 genes (measured with 59 probesets) were insignificant for survival (P&gt;0.05) in both data sets (Table 4). 
     Example 2 
     Actin B (ACTB) is among the genes most widely used as a reference in gene expression measurements with qRT-PCR. However, in the samples where CNV is observed within ACTB, using it as a reference increases the observed variation in the observed values of the copy number and gene expression of assessed genes. The example indicates that in EOC samples all genes of Actin family are characterized with a strong CNV ( FIG. 3 ). 
     Example 3 
     Genes, like ACTB, most commonly used as references for gene expression in normal samples, cannot be used as such in EOC samples both in the context of gene expression and copy number measurements, due to their essential CNV. Instead, reference genes should be selected firstly, based on the criteria of the minimal (or absent) CNV in the studied samples. A method implementing such selection is a part of the present invention. Only the genes with no CNV localized in cytobands with non-varying copy number are selected as CNV-invariant genes ( FIG. 4 ). Additionally, the genes whose expression are high and correlate across two EOC cohorts ( FIG. 5 ) are selected from the former list, as satisfying the criteria of both low CNV and high expression. The genes whose expression reveal a survival significance in any of the two studied patient cohorts, were excluded from the candidate reference gene list as potentially subjected to selective pressure. 
     Example 4 
     The processed DCHGV (A Deep Catalog of Human Genetic Variation, 1000 Genomes Project) [Abecasis G R, et al.,  Nature  467: 1061-1073 (2010); Mills R E, et al.,  Nature  470: 59-65 (2011)] data set containing 89076 frequent gain/loss genomic aberrations in 19354 genes across 1062 samples was used in the analysis. Genes located in CN-invariant cytobands (i.e. cytobands contained no genomic gains or losses) in EOC tumors (TCGA) were filtered through the list of genes with aberrations obtained from the DCHGV. The 41 genes found to be CN-invariant in the TCGA EOC samples, and whose CN at the same time seldomly changed across the 1062 samples of normal human tissues, were considered CN-stable. 
     Example 5 
     To validate the genes selected as CN-invariant in EOC tumors along with the algorithms for selection of such genes, the copy number and expression of a selected set of genes were measured with qRT-PCR in EOC tumors and normal tissues. The list of targets for validation included three genes most often used as expression references for qPCR experiments (ACTB, TBP, and GAPDH) and six genes obtained by using the algorithms described here (AUTS2, EIF5, FHL2, PARN, and YEATS2). 
     Two sets of primers were designed to detect the amplification of each of these genes in the qPCR reactions measuring either the CN or the expression values (Table 6). For further analyses primer set 2 was used. The primer melting curves demonstrate that all the primers have a single region of annealing in the human genome. Except for XRCC5, each primer pair demonstrates a single melting temperature within 75 to 90 degrees Celsius range ( FIG. 6 ). The existence of additional small-scale melting events in the XRCC5 primer pair could be explained by a secondary structure in one or both primers of the pair. This effect is commonly considered insignificant for the primer specificity and sensitivity. To test the reproducibility of the obtained qPCR signal, the CN ( FIGS. 7 and 9 ) and expression ( FIGS. 8 and 10 ) of the reference genes were tested. The results show that both in both types of measurements the proposed reference genes were not less reproducible than the genes traditionally used as gene expression references (ACTB, GAPDH, and TBP). 
     Example 6 
     To find whether the any of the traditional gene expression reference genes (ACTB, GAPDH, and TBP) could serve also as references for gene CN measurements, their CN distribution was evaluated across EOC tumor samples (TCGA cohort). The results demonstrate that CNV in these genes occur in 20 to 100 percent tumors, GAPDH tending to be amplified, and TBP to be deleted ( FIG. 11 ). 
     To assess the effect of the reference genes, the CN of MECOM locus (one of the most frequently amplified in EOC) was normalized by the CN of the reference genes. It would some aspects of a CN measurement with a qPCR-based technique, where the CT values of the target gene is normalized by the CT values of the reference gene ( FIG. 12 ). The results demonstrate that replacing ACTB with XRCC5 as a CN normalization reference increased the observed difference between the median MECOM CN in the tumors and the control samples ( FIGS. 12A ,D,F), decreased its variation in the tumor samples ( FIG. 12B ), and remained low in the tumor samples. For ACTB, EIF5, and XRCC5 the difference between the tumor and the control sample groups was significant (P&lt;0.05, Wilcoxon test;  FIG. 12A ). For AUTS2 a borderline significance (P=0.06) was observed. 
     Example 7 
     Ten most common cancers (Table 7), whose combined frequency account for 59% of all cancer cases worldwide, were selected, cross-validation of the loci serving as potential references for the Therascreen EGFR EGQ PCR kit (Qiagen). The six candidate reference loci proposed for ovarian cancer (see Table 6) were compared against ACTB, TBP, and GAPDH as potential normalization controls for the EGFR gene CN measurement ( FIG. 13 ). The results demonstrate that in 8 out of 10 most common cancers (all, except for the colon and cervical cancers, thus comprising over 50% of all cancer cases) the lowest variation of the EGFR CN measurement is obtained with normalization by one of the proposed reference genes, but not ‘traditional reference genes’. The 2 cases, where the ‘traditional references’ (specifically, ACTB) perform better are cervical squamous cell carcinoma and colon cancer. For 7 of 10 cases, the reference gene with the worst performance was among the ‘traditional reference genes’. For the lung adenocarcinoma samples, the normalization by all the candidate reference loci resulted in the EGFR variation to be lower than in the cases for any of the traditional control loci. For the ovarian serous adenocarcinoma samples, the median variation across values obtained by the candidate reference loci was more than two times lower than that obtained by the traditional control loci. 
     Example 8 
     Ten most common cancers (Table 7), whose combined frequency account for 59% of all cancer cases worldwide, were selected cross-validation of the loci serving as potential references for the Human Breast Cancer PCR array (Qiagen). The six candidate reference loci proposed for ovarian cancer (see Table 6) were compared against ACTB, TBP, and GAPDH as potential normalization controls for the CN measurements of the 23 diagnostic array loci (Table 12). Across the breast invasive carcinoma ( FIG. 14A ) and lung adenocarcinoma tumors ( FIG. 14B ), the lowest variation was revealed by one of the candidate reference loci for, at least, 22 out of the 23 loci of the diagnostic panel. When the median CN values across all the 23 panel loci were considered ( FIG. 15 ), the results qualitatively recapitulated the ones obtained with EGFR EGQ kit (in the Example 7) by demonstrating that in 8 out of 10 most common cancers the median variation across the test loci CN measurements was lower, when normalized by one of the ovarian cancer candidate reference loci, compared with any of the traditional control loci (ACTB, TBP, and GAPDH). 
     For the lung adenocarcinoma ( FIG. 14B ) and ovarian serous adenocarcinoma ( FIG. 18A ), for all 23 assay loci, the normalization by at least one of the candidate reference loci resulted in the assay loci variation to be lower than in the cases when any of the traditional control loci were used. For the ovarian serous adenocarcinoma samples, the median variation across values obtained by the candidate reference loci was more than two times lower than that obtained by the traditional control loci. 
     Across the breast invasive carcinoma ( FIG. 14A ), lung squamous cell carcinoma ( FIG. 16B ), head and neck squamous cell carcinoma ( FIG. 16A ), and prostate adenocarcinoma ( FIG. 18A ), for, at least, 22 loci of the diagnostic panel, the lowest variation of the assay loci was obtained by using one of the candidate reference loci, but not the traditional control loci. For liver hepatocellular carcinoma ( FIG. 18A ) and stomach adenocarcinoma ( FIG. 19A ) the respective improvement was detected for 20 assay loci. For colon adenocarcinoma ( FIG. 17B ) and cervical squamous cell carcinoma ( FIG. 19B ) the improvement was detected for 15 and 14 assay loci, respectively. 
     Example 9 
     An embodiment of the proposed method has been applied to select the candidate loci that could serve as common references to the ten most frequent cancers (Table 7) as follows. First, the loci with the lowest CN variation across the samples of each out of ten cancers ( FIG. 20 ) were identified. Thus, ten loci lists were selected. Next, the loci common across all the ten lists, 66 loci (Table 8 and  FIG. 20 ) were chosen as the reference candidates that can be used for normalization of the samples belonging to any of the ten selected cancers. 
     Example 10 
     An embodiment of the proposed method has been applied to select the candidate loci that could serve as common references for tissues from healthy subjects, patients with non-cancerous disease, and cancer-unaffected tissues obtained from cancer patients. The healthy subjects were represented by the 1000 genomes of DCHGV cohort [Abecasis G R, et al.,  Nature  467: 1061-1073 (2010); Mills R E, et al.,  Nature  470: 59-65 (2011)] obtained from various tissues. The genomes of the non-cancerous patients were represented by the blood samples of 31 myocardial infarction patients (data set GSE31276). 
     To assess the CNV in the genomes of the 5290 patients, affected by the 10 most frequent cancers (listed in Table 7), genomic data of Level 3 (as defined by the TCGA data processing methods) was obtained. Each patient was characterized with the genomic data obtained from a pair of a blood sample and a tumor sample. Analyses of the tumor samples of these patients are presented in the Examples 7-9 (the TCGA cohort). 
     The blood samples of these patients were considered as cancer-unaffected, along with the samples from the DCHGV and the GSE31276 cohorts. Our analysis demonstrated that the total number of loci with the lowest, effectively zero, variation in were 8300, 1231, and 16 loci in the DCHGV, the GSE31276, and the TCGA cohorts, respectively (Table 9;  FIG. 21 ). These three respective loci sets were suggested as cohort-specific sources of the reference loci. 
     In the intersections of these three sets, cross-cohort sources of reference loci were identified. A total of 637 loci revealed the lowest variance across both the DCHGV and the myocardial infarction patients&#39; blood genomes, were considered as reference control candidates for non-cancerous genomes (Table 10). 
     Thee loci (Table 11) are most stable across normal subject, non-cancerous disease subject, and cancer-unaffected tissues of cancer patients. They are regarded as candidate reference loci for CN normalization across all non-cancerous subjects. 
     Altogether, the cohort-specific and cross-cohort reference loci might be applied to study naturally occurring DNA copy number variations in the blood. These variations might be population-specific and reveal markers of various disease predispositions. 
     The present invention developed from work on DNA quantification with qPCR. The quantification procedure requires knowledge of both the target locus (or gene) of interest and the locus (or gene) of reference. The DNA of the target locus is quantified by the difference between the PCR amplification cycles counts of the target gene and the reference gene. The main assumption of the method is that for the reference gene the DNA copy number (and hence the PCR amplification cycles count) remains the same for all samples, including the tested and the control ones. In our work we found that this assumption does not hold true for, at least, cancer samples. Since the cancer genome is highly mobile, and its evolution is unpredictable, any gene in the genome can be either amplified or deleted in a large number of cells comprising the cancer cells population. We experimentally observed that this amplification results in highly varying DNA copy numbers of the traditional qPCR reference loci, ACTB and GAPDH. Therefore, we experimentally confirmed that the above assumption is invalid. Moreover, since the RNA level of a gene is a product of the DNA of the same gene (with a non-linear dependence of the former on the latter), the validity of any universal standard loci for RNA quantification is also compromised. 
     To select a locus suitable as a qPCR reference, we proposed to discard the assumption of a universal reference, and developed procedures that would identify the best reference for a given multitude of samples. For example, the multitude may be defined as ovarian cancer samples (such as in Examples 1, 2, and 3). If we define that the best reference locus (or gene) is a locus, whose DNA copy number value, as measured in a given qPCR setup, simultaneously satisfies two or more conditions: 1) has the smallest variation in all the samples (the specificity criterion), 2) can be detected in all the samples, and/or 3) should not evolve with time or as a result of environmental condition changes (e.g. disease treatments). In patients, the third condition can be ensured by neutrality of the gene&#39;s copy number and expression to the patient survival. Thus, the definition of the best reference set dictates the criteria for an unbiased selection of the reference genes. We implemented a computational pipeline ( FIGS. 4 and 5 ) that allowed us to scan through publicly available data on ovarian cancer samples and select a list of such candidate reference loci (given in Table 1; see also Example 1). 
     We carried out an experimental study to check whether the present most popular control loci (ACTB, GAPDH, TBP) satisfy the above conditions and how they compare to the list (Table 1) obtained with our unbiased selection method (see Example 5). We confirmed that: 1) the universal reference assumption does not hold true, since both ACTB and GAPDH reveal DNA copy number variation ( FIGS. 3 and 11 ); 2) the unbiased search for ovarian cancer-specific reference loci provided the candidates, which satisfy the above reference criteria better than the TBP locus (Tables 1 and 4;  FIGS. 7, 9, 11 ); 3) our method provides the best reference loci not only for DNA copy number (qPCR), but also expression measurements (Tables 2 and 3;  FIGS. 8 and 10 ). To check these results in a real case scenario, we used our candidate reference loci, along with the traditional reference loci (ACTB, GAPDH, and TBP) to measure the DNA copy number and expression of the EVI1 gene of the MECOM complex locus (Example 6). We concluded that using of our candidate loci as references resulted in lower variations MECOM DNA copy number and RNA expression measurements, compared to the case, when the traditional reference loci were used (Example 6;  FIG. 12 ). We also concluded that our experimental result validate our use of publicly available high-throughput data sets as the entry points for our computational pipeline. 
     To further predict the performance of our tests for the cases of other cancers and non-cancerous diseases, we carried out a computational study using publicly available high-throughput data obtained from patients diagnosed with ten most common cancer types (Examples 7, 8, and 9), myocardial infarction (Example 10), and a selection of healthy DNA donors from multiple populations across the world (Example 10). We also demonstrated how application of our method can improve the variability of the measurements obtained with two popular in-vitro diagnostic tests (Examples 7 and 8;  FIGS. 13-20 ). 
     Materials and Methods 
     CGH Microarray Data Analysis 
     The publicly available Affymetrix SNP-6.0 microarray data (described in the Clinical data section) was retrieved from the Gene Expression Omnibus (GEO) repsitory. Each data set was independently normalized using the following steps: 
     Clinical Data. 
     The initial data analysis was carried out with publicly available datasets: TCGA (The Cancer Genome Atlas) [Bell D, et al.,  Nature  474: 609-15 (2011)], GSE9899 [Tothill R W, et al.,  Clin Cancer Res  14: 5198-5208 (2008)], and DCHGV (A Deep Catalog of Human Genetic Variation, 1000 Genomes Project) [Abecasis G R, et al.,  Nature  467: 1061-1073 (2010); Mills R E, et al.,  Nature  470: 59-65 (2011)]. 
     The National Institute of Health (NIH) Cancer Genome Atlas (TCGA) data set with 514 EOC patients was used for the analysis of CNV, gene expression and patient survival [Bell D, et al.,  Nature  474: 609-15 (2011)]. The patients, which EOC tumors had EVI1 gene amplified (average EVI1 gene copy number not less than 2.5 per cell), defined here as ‘EVI1 amplified group, were analyzed separately. The 5-year survival for this group of patients was 36 percent. The 5-year survival of the whole patient cohort was 28 percent. The 2-year survival of the whole patient cohort was 74 percent. Gene expression was measured with Affymetrix U133-A microarrays. Copy number was measured with Affymetrix SNP-6.0 CGH microarrays. 
     Gene Expression Omnibus (NIH) repository was used to obtain the GSE9899 (accession number) data set containing 246 samples [Tothill R W, et al.,  Clin Cancer Res  14: 5198-5208 (2008)]. From this set 16 patients were removed after a quality control assessment. The 5-year survival of the whole patient cohort was 44 percent. The 2-year survival of the whole patient cohort was 57 percent. Gene expression was measured with Affymetrix U133-Plus-2.0 microarrays. 
     A Deep Catalog of Human Genetic Variation (DCHGV) was used to obtain data on 202430 natural variations in the human genome reported in 10692 normal human tissue samples. Only variations reported as genomic gains or losses in more than 10 samples at frequencies more than 10% were included in the analysis. In total, 89076 genetic variations were selected, including 24891 cases of genomic gains and 64185 losses in 19354 genes, across 10692 biological samples. 
     Gene Expression Omnibus (NIH) repository was used to obtain the GSE31276 data set containing 31 individual genome profiles obtained from the blood of myocardial infarction patients. The samples were collected according to the Prospective Cardiovascular Munster study [Assmann G and Schulte H  American heart journal  116: 1713-24 (1988)] and Framingham Heart study [Benjamin E J, et al.,  Circulation  98: 946-52 (1998)]. 
     For validation experiments 48 DNA samples and 80 RNA samples purchased from Origene were used. The 48 DNA samples were extracted from individual serous ovarian adenocarcinoma tumors obtained from: 4 patients with the disease at stage 1, 3 patients at stage 2, 34 patients at stage 3, and 2 patients at stage 4. The 80 RNA samples were extracted from 7 normal fallopian tubes, 21 normal ovaries, and 52 individual serous ovarian adenocarcinoma tumors. The tumors were obtained from 11 patients with the disease at stage 1, 7 patients at stage 2, 29 patients at stage 3, and 5 patients at stage 4. For all 80 RNA samples the cDNA was synthesized using QuantiTect Reverse Transcription Kit 200 (Qiagen; cat. no: 205313). 
     Tables 
       
     
       
         
           
               
             
               
                 TABLE 1 
               
             
            
               
                   
               
               
                 Genes with invariant copy numbers across TCGA cohorts 
               
            
           
           
               
               
               
               
               
               
            
               
                 Symbol 
                 Refseq 
                 Chr 
                 Start 
                 End 
                 Description 
               
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 ABCB4 
                 NM_018849 
                 chr7 
                 87031360 
                 87105019 
                 multidrug resistance 
               
               
                   
                   
                   
                   
                   
                 protein 3 isoform B 
               
               
                 ABHD5 
                 NM_016006 
                 chr3 
                 43732374 
                 43764217 
                 1-acylglycerol-3- 
               
               
                   
                   
                   
                   
                   
                 phosphate O- 
               
               
                   
                   
                   
                   
                   
                 acyltransferase ABHD5 
               
               
                 ACYP2 
                 NM_138448 
                 chr2 
                 54342409 
                 54532435 
                 acylphosphatase-2 
               
               
                 AFF3 
                 NM_001025108 
                 chr2 
                 100163715 
                 100722045 
                 AF4/FMR2 family 
               
               
                   
                   
                   
                   
                   
                 member 3 isoform 2 
               
               
                 AGAP1 
                 NM_001244888 
                 chr2 
                 236402732 
                 236761846 
                 arf-GAP with GTPase, 
               
               
                   
                   
                   
                   
                   
                 ANK repeat and PH 
               
               
                   
                   
                   
                   
                   
                 domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 1 isoform 3 
               
               
                 AGBL4 
                 NM_032785 
                 chr1 
                 48998526 
                 50489626 
                 cytosolic 
               
               
                   
                   
                   
                   
                   
                 carboxypeptidase 6 
               
               
                 AMD1 
                 NM_001287216 
                 chr6 
                 111195986 
                 111216915 
                 S-adenosylmethionine 
               
               
                   
                   
                   
                   
                   
                 decarboxylase 
               
               
                   
                   
                   
                   
                   
                 proenzyme isoform 5 
               
               
                 ANK2 
                 NM_001127493 
                 chr4 
                 113739238 
                 114304896 
                 ankyrin-2 isoform 3 
               
               
                 ARSE 
                 NM_001282628 
                 chrX 
                 2852672 
                 2882494 
                 arylsulfatase E isoform 
               
               
                   
                   
                   
                   
                   
                 1 
               
               
                 ASAP1 
                 NM_018482 
                 chr8 
                 131064350 
                 131455906 
                 arf-GAP with SH3 
               
               
                   
                   
                   
                   
                   
                 domain, ANK repeat 
               
               
                   
                   
                   
                   
                   
                 and PH domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 1 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 ASCC3 
                 NM_001284271 
                 chr6 
                 101163006 
                 101329248 
                 activating signal 
               
               
                   
                   
                   
                   
                   
                 cointegrator 1 complex 
               
               
                   
                   
                   
                   
                   
                 subunit 3 isoform c 
               
               
                 ATAD2B 
                 NM_001242338 
                 chr2 
                 23971533 
                 24149984 
                 ATPase family AAA 
               
               
                   
                   
                   
                   
                   
                 domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 2B isoform 2 
               
               
                 ATF7IP2 
                 NM_024997 
                 chr16 
                 10479911 
                 10577495 
                 activating transcription 
               
               
                   
                   
                   
                   
                   
                 factor 7-interacting 
               
               
                   
                   
                   
                   
                   
                 protein 2 isoform 1 
               
               
                 ATXN7 
                 NM_001128149 
                 chr3 
                 63953419 
                 63989136 
                 ataxin-7 isoform c 
               
               
                 AUTS2 
                 NM_015570 
                 chr7 
                 69063904 
                 70258054 
                 autism susceptibility 
               
               
                   
                   
                   
                   
                   
                 gene 2 protein isoform 1 
               
               
                 AZIN2 
                 NM_052998 
                 chr1 
                 33546713 
                 33586132 
                 antizyme inhibitor 2 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 BATF3 
                 NM_018664 
                 chr1 
                 212859758 
                 212873327 
                 basic leucine zipper 
               
               
                   
                   
                   
                   
                   
                 transcriptional factor 
               
               
                   
                   
                   
                   
                   
                 ATF-like 3 
               
               
                 BMPR2 
                 NM_001204 
                 chr2 
                 203241049 
                 203432474 
                 bone morphogenetic 
               
               
                   
                   
                   
                   
                   
                 protein receptor type-2 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 BTLA 
                 NM_001085357 
                 chr3 
                 112182812 
                 112218408 
                 B- and T-lymphocyte 
               
               
                   
                   
                   
                   
                   
                 attenuator isoform 2 
               
               
                 BTNL8 
                 NM_001159707 
                 chr5 
                 180326076 
                 180377906 
                 butyrophilin-like protein 
               
               
                   
                   
                   
                   
                   
                 8 isoform 3 precursor 
               
               
                 C1orf21 
                 NM_030806 
                 chr1 
                 184356149 
                 184598155 
                 uncharacterized protein 
               
               
                   
                   
                   
                   
                   
                 C1orf21 
               
               
                 C4orf22 
                 NM_001206997 
                 chr4 
                 81256873 
                 81884910 
                 uncharacterized protein 
               
               
                   
                   
                   
                   
                   
                 C4orf22 isoform 1 
               
               
                 C4orf33 
                 NM_173487 
                 chr4 
                 130014828 
                 130033843 
                 UPF0462 protein 
               
               
                   
                   
                   
                   
                   
                 C4orf33 
               
               
                 CACNB2 
                 NM_201571 
                 chr10 
                 18429741 
                 18830688 
                 voltage-dependent L- 
               
               
                   
                   
                   
                   
                   
                 type calcium channel 
               
               
                   
                   
                   
                   
                   
                 subunit beta-2 isoform 6 
               
               
                 CADM2 
                 NM_153184 
                 chr3 
                 85775631 
                 86123579 
                 cell adhesion molecule 2 
               
               
                   
                   
                   
                   
                   
                 isoform 3 precursor 
               
               
                 CAMTA1 
                 NR_038934 
                 chr1 
                 6845383 
                 6948261 
               
               
                 CASC5 
                 NM_170589 
                 chr15 
                 40886446 
                 40954881 
                 protein CASC5 isoform 
               
               
                   
                   
                   
                   
                   
                 1 
               
               
                 CASQ2 
                 NM_001232 
                 chr1 
                 116242625 
                 116311426 
                 calsequestrin-2 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 CCDC88A 
                 NM_018084 
                 chr2 
                 55514977 
                 55647057 
                 girdin isoform 2 
               
               
                 CHL1 
                 NR_045572 
                 chr3 
                 239325 
                 290282 
               
               
                 CHST15 
                 NM_014863 
                 chr10 
                 125779168 
                 125851940 
                 carbohydrate 
               
               
                   
                   
                   
                   
                   
                 sulfotransferase 15 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 CLASP1 
                 NM_001142273 
                 chr2 
                 122095351 
                 122407052 
                 CLIP-associating 
               
               
                   
                   
                   
                   
                   
                 protein 1 isoform 2 
               
               
                 CLIC4 
                 NM_013943 
                 chr1 
                 25071759 
                 25170815 
                 chloride intracellular 
               
               
                   
                   
                   
                   
                   
                 channel protein 4 
               
               
                 CLMN 
                 NM_024734 
                 chr14 
                 95648275 
                 95786245 
                 calmin 
               
               
                 CNTN3 
                 NM_020872 
                 chr3 
                 74311721 
                 74570343 
                 contactin-3 precursor 
               
               
                 COPA 
                 NM_001098398 
                 chr1 
                 160258376 
                 160313354 
                 coatomer subunit alpha 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 CTTNBP2 
                 NM_033427 
                 chr7 
                 117350705 
                 117513561 
                 cortactin-binding 
               
               
                   
                   
                   
                   
                   
                 protein 2 
               
               
                 CUL3 
                 NM_001257197 
                 chr2 
                 225334866 
                 225450114 
                 cullin-3 isoform 2 
               
               
                 DAB1 
                 NM_021080 
                 chr1 
                 57463578 
                 58716211 
                 disabled homolog 1 
               
               
                 DAPK1 
                 NM_001288729 
                 chr9 
                 90113449 
                 90323549 
                 death-associated protein 
               
               
                   
                   
                   
                   
                   
                 kinase 1 
               
               
                 DDAH1 
                 NM_012137 
                 chr1 
                 85784167 
                 85930889 
                 N(G),N(G)- 
               
               
                   
                   
                   
                   
                   
                 dimethylarginine 
               
               
                   
                   
                   
                   
                   
                 dimethylaminohydrolase 
               
               
                   
                   
                   
                   
                   
                 1 isoform 1 
               
               
                 DEGS1 
                 NM_003676 
                 chr1 
                 224370909 
                 224381142 
                 sphingolipid delta(4)- 
               
               
                   
                   
                   
                   
                   
                 desaturase DES1 
               
               
                 DEPDC1 
                 NM_001114120 
                 chr1 
                 68939834 
                 68962904 
                 DEP domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 1A isoform a 
               
               
                 DGAT2 
                 NM_001253891 
                 chr11 
                 75479777 
                 75512581 
                 diacylglycerol O- 
               
               
                   
                   
                   
                   
                   
                 acyltransferase 2 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 DNM3 
                 NM_015569 
                 chr1 
                 171810617 
                 172381857 
                 dynamin-3 isoform a 
               
               
                 DPP10 
                 NM_001178034 
                 chr2 
                 115919512 
                 116602326 
                 inactive dipeptidyl 
               
               
                   
                   
                   
                   
                   
                 peptidase 10 isoform c 
               
               
                 DPPA4 
                 NM_018189 
                 chr3 
                 109044987 
                 109056419 
                 developmental 
               
               
                   
                   
                   
                   
                   
                 pluripotency-associated 
               
               
                   
                   
                   
                   
                   
                 protein 4 
               
               
                 DYRK1A 
                 NM_001396 
                 chr21 
                 38792601 
                 38887679 
                 dual specificity tyrosine- 
               
               
                   
                   
                   
                   
                   
                 phosphorylation- 
               
               
                   
                   
                   
                   
                   
                 regulated kinase 1A 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 EFHC2 
                 NM_025184 
                 chrX 
                 44007127 
                 44202923 
                 EF-hand domain- 
               
               
                   
                   
                   
                   
                   
                 containing family 
               
               
                   
                   
                   
                   
                   
                 member C2 
               
               
                 EHBP1 
                 NM_015252 
                 chr2 
                 62933000 
                 63273621 
                 EH domain-binding 
               
               
                   
                   
                   
                   
                   
                 protein 1 isoform 1 
               
               
                 EHD3 
                 NM_014600 
                 chr2 
                 31456879 
                 31491260 
                 EH domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 3 
               
               
                 EIF5 
                 NM_001969 
                 chr14 
                 103800338 
                 103811361 
                 eukaryotic translation 
               
               
                   
                   
                   
                   
                   
                 initiation factor 5 
               
               
                 EMX2OS 
                 NR_002791 
                 chr10 
                 119243803 
                 119304579 
               
               
                 ENPP2 
                 NR_045555 
                 chr8 
                 120569316 
                 120605248 
               
               
                 EPB41 
                 NM_001166007 
                 chr1 
                 29213602 
                 29446558 
                 protein 4.1 isoform 5 
               
               
                 EPHB2 
                 NM_004442 
                 chr1 
                 23037330 
                 23241823 
                 ephrin type-B receptor 2 
               
               
                   
                   
                   
                   
                   
                 isoform 2 precursor 
               
               
                 ERBB4 
                 NM_005235 
                 chr2 
                 212240441 
                 213403352 
                 receptor tyrosine-protein 
               
               
                   
                   
                   
                   
                   
                 kinase erbB-4 isoform 
               
               
                   
                   
                   
                   
                   
                 JM-a/CVT-1 precursor 
               
               
                 ERC2 
                 NM_015576 
                 chr3 
                 55542335 
                 56502391 
                 ERC protein 2 
               
               
                 ESRRG 
                 NM_206594 
                 chr1 
                 216676587 
                 217262987 
                 estrogen-related 
               
               
                   
                   
                   
                   
                   
                 receptor gamma isoform 
               
               
                   
                   
                   
                   
                   
                 2 
               
               
                 FAHD2A 
                 NM_016044 
                 chr2 
                 96068447 
                 96078879 
                 fumarylacetoacetate 
               
               
                   
                   
                   
                   
                   
                 hydrolase domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 2A 
               
               
                 FAM132B 
                 NM_001291832 
                 chr2 
                 239067648 
                 239077532 
                 erythroferrone precursor 
               
               
                 FAM135B 
                 NM_015912 
                 chr8 
                 139142265 
                 139509065 
                 protein FAM135B 
               
               
                 FAM49A 
                 NM_030797 
                 chr2 
                 16730729 
                 16847134 
                 protein FAM49A 
               
               
                 FAT1 
                 NM_005245 
                 chr4 
                 187508936 
                 187644987 
                 protocadherin Fat 1 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 FBXO32 
                 NM_058229 
                 chr8 
                 124510126 
                 124553493 
                 F-box only protein 32 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 FCGR2A 
                 NM_001136219 
                 chr1 
                 161475204 
                 161489360 
                 low affinity 
               
               
                   
                   
                   
                   
                   
                 immunoglobulin gamma 
               
               
                   
                   
                   
                   
                   
                 Fc region receptor II-a 
               
               
                   
                   
                   
                   
                   
                 isoform 1 precursor 
               
               
                 FGF12 
                 NM_004113 
                 chr3 
                 191857181 
                 192445388 
                 fibroblast growth factor 
               
               
                   
                   
                   
                   
                   
                 12 isoform 2 
               
               
                 FGGY 
                 NM_001113411 
                 chr1 
                 59762624 
                 60228402 
                 FGGY carbohydrate 
               
               
                   
                   
                   
                   
                   
                 kinase domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 
               
               
                   
                   
                   
                   
                   
                 isoform a 
               
               
                 FHIT 
                 NM_002012 
                 chr3 
                 59735035 
                 61237133 
                 bis(5′-adenosyl)- 
               
               
                   
                   
                   
                   
                   
                 triphosphatase 
               
               
                 FHL1 
                 NM_001159702 
                 chrX 
                 135229558 
                 135293518 
                 four and a half LIM 
               
               
                   
                   
                   
                   
                   
                 domains protein 1 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 FHL2 
                 NM_201557 
                 chr2 
                 105977282 
                 106055230 
                 four and a half LIM 
               
               
                   
                   
                   
                   
                   
                 domains protein 2 
               
               
                 FOXP1 
                 NM_001012505 
                 chr3 
                 71247033 
                 71633140 
                 forkhead box protein P1 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 FRMD3 
                 NM_001244959 
                 chr9 
                 85857904 
                 86153348 
                 FERM domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 3 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 FUT9 
                 NM_006581 
                 chr6 
                 96463844 
                 96663488 
                 alpha-(1,3)- 
               
               
                   
                   
                   
                   
                   
                 fucosyltransferase 9 
               
               
                 GADL1 
                 NM_207359 
                 chr3 
                 30767691 
                 30936153 
                 acidic amino acid 
               
               
                   
                   
                   
                   
                   
                 decarboxylase GADL1 
               
               
                 GAP43 
                 NM_002045 
                 chr3 
                 115342150 
                 115440334 
                 neuromodulin isoform 2 
               
               
                 GBAP1 
                 NR_002188 
                 chr1 
                 155183615 
                 155197325 
               
               
                 GBE1 
                 NM_000158 
                 chr3 
                 81538849 
                 81810950 
                 1,4-alpha-glucan- 
               
               
                   
                   
                   
                   
                   
                 branching enzyme 
               
               
                 GLI2 
                 NM_005270 
                 chr2 
                 121554866 
                 121750229 
                 zinc finger protein GLI2 
               
               
                 GOLIM4 
                 NM_014498 
                 chr3 
                 167727653 
                 167813417 
                 Golgi integral 
               
               
                   
                   
                   
                   
                   
                 membrane protein 4 
               
               
                 GPBP1L1 
                 NM_021639 
                 chr1 
                 46092975 
                 46152302 
                 vasculin-like protein 1 
               
               
                 GRM8 
                 NM_001127323 
                 chr7 
                 126078651 
                 126892428 
                 metabotropic glutamate 
               
               
                   
                   
                   
                   
                   
                 receptor 8 isoform b 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 GTF2F2 
                 NM_004128 
                 chr13 
                 45694630 
                 45858239 
                 general transcription 
               
               
                   
                   
                   
                   
                   
                 factor IIF subunit 2 
               
               
                 H6PD 
                 NM_001282587 
                 chr1 
                 9299902 
                 9331394 
                 GDH/6PGL 
               
               
                   
                   
                   
                   
                   
                 endoplasmic 
               
               
                   
                   
                   
                   
                   
                 bifunctional protein 
               
               
                   
                   
                   
                   
                   
                 isoform 1 precursor 
               
               
                 HHAT 
                 NM_001122834 
                 chr1 
                 210501595 
                 210849638 
                 protein-cysteine N- 
               
               
                   
                   
                   
                   
                   
                 palmitoyltransferase 
               
               
                   
                   
                   
                   
                   
                 HHAT isoform 1 
               
               
                 HS3ST1 
                 NM_005114 
                 chr4 
                 11399987 
                 11430537 
                 heparan sulfate 
               
               
                   
                   
                   
                   
                   
                 glucosamine 3-O- 
               
               
                   
                   
                   
                   
                   
                 sulfotransferase 1 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 HTR4 
                 NM_199453 
                 chr5 
                 147830594 
                 148016624 
                 5-hydroxytryptamine 
               
               
                   
                   
                   
                   
                   
                 receptor 4 isoform g 
               
               
                 HYAL3 
                 NM_003549 
                 chr3 
                 50330258 
                 50336899 
                 hyaluronidase-3 isoform 
               
               
                   
                   
                   
                   
                   
                 1 precursor 
               
               
                 IDO2 
                 NM_194294 
                 chr8 
                 39792473 
                 39873910 
                 indoleamine 2,3- 
               
               
                   
                   
                   
                   
                   
                 dioxygenase 2 
               
               
                 IGSF11 
                 NM_152538 
                 chr3 
                 118619478 
                 118864898 
                 immunoglobulin 
               
               
                   
                   
                   
                   
                   
                 superfamily member 11 
               
               
                   
                   
                   
                   
                   
                 isoform a precursor 
               
               
                 IL15 
                 NR_037840 
                 chr4 
                 142557748 
                 142655140 
               
               
                 IL5RA 
                 NM_175726 
                 chr3 
                 3108007 
                 3152058 
                 interleukin-5 receptor 
               
               
                   
                   
                   
                   
                   
                 subunit alpha isoform 1 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 IQGAP3 
                 NM_178229 
                 chr1 
                 156495196 
                 156542396 
                 ras GTPase-activating- 
               
               
                   
                   
                   
                   
                   
                 like protein IQGAP3 
               
               
                 KCNAB1 
                 NM_172159 
                 chr3 
                 156008775 
                 156256927 
                 voltage-gated potassium 
               
               
                   
                   
                   
                   
                   
                 channel subunit beta-1 
               
               
                   
                   
                   
                   
                   
                 isoform 3 
               
               
                 KCNIP4 
                 NM_147183 
                 chr4 
                 20730238 
                 21305529 
                 Kv channel-interacting 
               
               
                   
                   
                   
                   
                   
                 protein 4 isoform 4 
               
               
                 LAMC3 
                 NM_006059 
                 chr9 
                 133884503 
                 133968446 
                 laminin subunit gamma- 
               
               
                   
                   
                   
                   
                   
                 3 precursor 
               
               
                 LDB2 
                 NM_001290 
                 chr4 
                 16503164 
                 16900424 
                 LIM domain-binding 
               
               
                   
                   
                   
                   
                   
                 protein 2 isoform a 
               
               
                 LEF1 
                 NM_001130714 
                 chr4 
                 108968700 
                 109090112 
                 lymphoid enhancer- 
               
               
                   
                   
                   
                   
                   
                 binding factor 1 isoform 
               
               
                   
                   
                   
                   
                   
                 3 
               
               
                 LIN54 
                 NM_001115008 
                 chr4 
                 83845756 
                 83931987 
                 protein lin-54 homolog 
               
               
                   
                   
                   
                   
                   
                 isoform b 
               
               
                 LIN9 
                 NM_001270410 
                 chr1 
                 226418849 
                 226497449 
                 protein lin-9 homolog 
               
               
                   
                   
                   
                   
                   
                 isoform 3 
               
               
                 LOC100506122 
                 NR_038838 
                 chr4 
                 171961752 
                 171980311 
               
               
                 LOC100506457 
                 NR_110198 
                 chr2 
                 12147241 
                 12223743 
               
               
                 LOC101926942 
                 NR_110657 
                 chr10 
                 92162277 
                 92300562 
               
               
                 LOC101927905 
                 NR_120455 
                 chr12 
                 8388010 
                 8391553 
               
               
                 LPHN3 
                 NM_015236 
                 chr4 
                 62362838 
                 62938168 
                 latrophilin-3 precursor 
               
               
                 LRCH1 
                 NM_015116 
                 chr13 
                 47127295 
                 47319036 
                 leucine-rich repeat and 
               
               
                   
                   
                   
                   
                   
                 calponin homology 
               
               
                   
                   
                   
                   
                   
                 domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 1 isoform 2 
               
               
                 LRP1B 
                 NM_018557 
                 chr2 
                 140988995 
                 142889270 
                 low-density lipoprotein 
               
               
                   
                   
                   
                   
                   
                 receptor-related protein 
               
               
                   
                   
                   
                   
                   
                 1B precursor 
               
               
                 LRRC8C 
                 NM_032270 
                 chr1 
                 90098643 
                 90185094 
                 volume-regulated anion 
               
               
                   
                   
                   
                   
                   
                 channel subunit 
               
               
                   
                   
                   
                   
                   
                 LRRC8C 
               
               
                 LYST 
                 NM_001301365 
                 chr1 
                 235824330 
                 236047008 
                 lysosomal-trafficking 
               
               
                   
                   
                   
                   
                   
                 regulator 
               
               
                 LZTS2 
                 NM_032429 
                 chr10 
                 102756863 
                 102767593 
                 leucine zipper putative 
               
               
                   
                   
                   
                   
                   
                 tumor suppressor 2 
               
               
                 MALRD1 
                 NM_001142308 
                 chr10 
                 19337699 
                 20023407 
                 MAM and LDL- 
               
               
                   
                   
                   
                   
                   
                 receptor class A 
               
               
                   
                   
                   
                   
                   
                 domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 1 precursor 
               
               
                 MAN1A1 
                 NM_005907 
                 chr6 
                 119498365 
                 119670931 
                 mannosyl- 
               
               
                   
                   
                   
                   
                   
                 oligosaccharide 1,2- 
               
               
                   
                   
                   
                   
                   
                 alpha-mannosidase IA 
               
               
                 MCHR2 
                 NM_001040179 
                 chr6 
                 100367785 
                 100442099 
                 melanin-concentrating 
               
               
                   
                   
                   
                   
                   
                 hormone receptor 2 
               
               
                 MCTP1 
                 NM_001002796 
                 chr5 
                 94041241 
                 94417570 
                 multiple C2 and 
               
               
                   
                   
                   
                   
                   
                 transmembrane domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 1 
               
               
                   
                   
                   
                   
                   
                 isoform S 
               
               
                 MFAP3L 
                 NM_021647 
                 chr4 
                 170907747 
                 170947581 
                 microfibrillar-associated 
               
               
                   
                   
                   
                   
                   
                 protein 3-like isoform 1 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 MIR5694 
                 NR_049879 
                 chr10 
                 122344590 
                 122806858 
               
               
                 MORC3 
                 NM_015358 
                 chr21 
                 37692486 
                 37748944 
                 MORC family CW-type 
               
               
                   
                   
                   
                   
                   
                 zinc finger protein 3 
               
               
                 MRPL47 
                 NM_020409 
                 chr3 
                 179306254 
                 179322434 
                 39S ribosomal protein 
               
               
                   
                   
                   
                   
                   
                 L47, mitochondrial 
               
               
                   
                   
                   
                   
                   
                 isoform a 
               
               
                 MTA1 
                 NM_001203258 
                 chr14 
                 105886185 
                 105937057 
                 metastasis-associated 
               
               
                   
                   
                   
                   
                   
                 protein MTA1 isoform 
               
               
                   
                   
                   
                   
                   
                 MTA1s 
               
               
                 NAA16 
                 NM_024561 
                 chr13 
                 41885340 
                 41951166 
                 N-alpha- 
               
               
                   
                   
                   
                   
                   
                 acetyltransferase 16, 
               
               
                   
                   
                   
                   
                   
                 NatA auxiliary subunit 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 NBPF8 
                 NR_102404 
                 chr1 
                 147574322 
                 148346929 
               
               
                 NCOA7 
                 NM_001199619 
                 chr6 
                 126102306 
                 126253176 
                 nuclear receptor 
               
               
                   
                   
                   
                   
                   
                 coactivator 7 isoform 1 
               
               
                 NECAP2 
                 NM_001145278 
                 chr1 
                 16767166 
                 16786584 
                 adaptin ear-binding 
               
               
                   
                   
                   
                   
                   
                 coat-associated protein 2 
               
               
                   
                   
                   
                   
                   
                 isoform 3 
               
               
                 NEGR1 
                 NM_173808 
                 chr1 
                 71868624 
                 72748277 
                 neuronal growth 
               
               
                   
                   
                   
                   
                   
                 regulator 1 precursor 
               
               
                 NEIL3 
                 NM_018248 
                 chr4 
                 178230990 
                 178284092 
                 endonuclease 8-like 3 
               
               
                 NLGN4X 
                 NM_181332 
                 chrX 
                 5808066 
                 6146923 
                 neuroligin-4, X-linked 
               
               
                 NMD3 
                 NM_015938 
                 chr3 
                 160939098 
                 160969795 
                 60S ribosomal export 
               
               
                   
                   
                   
                   
                   
                 protein NMD3 
               
               
                 NOTCH2 
                 NM_024408 
                 chr1 
                 120454175 
                 120612317 
                 neurogenic locus notch 
               
               
                   
                   
                   
                   
                   
                 homolog protein 2 
               
               
                   
                   
                   
                   
                   
                 isoform 1 preproprotein 
               
               
                 NRP2 
                 NM_018534 
                 chr2 
                 206547223 
                 206641880 
                 neuropilin-2 isoform 4 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 NRXN1 
                 NM_004801 
                 chr2 
                 50145642 
                 51259674 
                 neurexin-1-beta isoform 
               
               
                   
                   
                   
                   
                   
                 alpha 1 precursor 
               
               
                 NT5C2 
                 NM_001134373 
                 chr10 
                 104847773 
                 104953063 
                 cytosolic purine 5′- 
               
               
                   
                   
                   
                   
                   
                 nucleotidase 
               
               
                 NTNG1 
                 NM_014917 
                 chr1 
                 107682744 
                 108024475 
                 netrin-G1 isoform 3 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 NUP133 
                 NM_018230 
                 chr1 
                 229577043 
                 229644088 
                 nuclear pore complex 
               
               
                   
                   
                   
                   
                   
                 protein Nup133 
               
               
                 NYAP2 
                 NM_020864 
                 chr2 
                 226265601 
                 226518734 
                 neuronal tyrosine- 
               
               
                   
                   
                   
                   
                   
                 phosphorylated 
               
               
                   
                   
                   
                   
                   
                 phosphoinositide-3- 
               
               
                   
                   
                   
                   
                   
                 kinase adapter 2 
               
               
                 OLFM3 
                 NM_058170 
                 chr1 
                 102268122 
                 102462790 
                 noelin-3 isoform 2 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 OSBPL5 
                 NM_145638 
                 chr11 
                 3108345 
                 3186582 
                 oxysterol-binding 
               
               
                   
                   
                   
                   
                   
                 protein-related protein 5 
               
               
                   
                   
                   
                   
                   
                 isoform b 
               
               
                 PARN 
                 NM_001134477 
                 chr16 
                 14529556 
                 14724128 
                 poly(A)-specific 
               
               
                   
                   
                   
                   
                   
                 ribonuclease PARN 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 PCDH10 
                 NM_020815 
                 chr4 
                 134070469 
                 134074404 
                 protocadherin-10 
               
               
                   
                   
                   
                   
                   
                 isoform 2 precursor 
               
               
                 PCDH7 
                 NM_032456 
                 chr4 
                 30722029 
                 30726957 
                 protocadherin-7 isoform 
               
               
                   
                   
                   
                   
                   
                 b precursor 
               
               
                 PCOLCE2 
                 NM_013363 
                 chr3 
                 142536701 
                 142608045 
                 procollagen C- 
               
               
                   
                   
                   
                   
                   
                 endopeptidase enhancer 
               
               
                   
                   
                   
                   
                   
                 2 precursor 
               
               
                 PDE2A 
                 NM_001146209 
                 chr11 
                 72287183 
                 72380108 
                 cGMP-dependent 3′,5′- 
               
               
                   
                   
                   
                   
                   
                 cyclic 
               
               
                   
                   
                   
                   
                   
                 phosphodiesterase 
               
               
                   
                   
                   
                   
                   
                 isoform PDE2A4 
               
               
                 PDE6C 
                 NM_006204 
                 chr10 
                 95372344 
                 95425429 
                 cone cGMP-specific 
               
               
                   
                   
                   
                   
                   
                 3′,5′-cyclic 
               
               
                   
                   
                   
                   
                   
                 phosphodiesterase 
               
               
                   
                   
                   
                   
                   
                 subunit alpha&#39; 
               
               
                 PDIA3 
                 NM_005313 
                 chr15 
                 44038589 
                 44064804 
                 protein disulfide- 
               
               
                   
                   
                   
                   
                   
                 isomerase A3 precursor 
               
               
                 PDZK1 
                 NM_001201325 
                 chr1 
                 145727665 
                 145764206 
                 Na(+)/H(+) exchange 
               
               
                   
                   
                   
                   
                   
                 regulatory cofactor 
               
               
                   
                   
                   
                   
                   
                 NHE-KF3 isoform 1 
               
               
                 PHTF1 
                 NM_006608 
                 chr1 
                 114239823 
                 114301777 
                 putative homeodomain 
               
               
                   
                   
                   
                   
                   
                 transcription factor 1 
               
               
                 PLEKHA2 
                 NM_021623 
                 chr8 
                 38758752 
                 38831430 
                 pleckstrin homology 
               
               
                   
                   
                   
                   
                   
                 domain-containing 
               
               
                   
                   
                   
                   
                   
                 family A member 2 
               
               
                 POU2F1 
                 NM_001198783 
                 chr1 
                 167298280 
                 167396582 
                 POU domain, class 2, 
               
               
                   
                   
                   
                   
                   
                 transcription factor 1 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 PRDM16 
                 NM_022114 
                 chr1 
                 2985741 
                 3355185 
                 PR domain zinc finger 
               
               
                   
                   
                   
                   
                   
                 protein 16 isoform 1 
               
               
                 PRDM5 
                 NM_001300824 
                 chr4 
                 121613067 
                 121844021 
                 PR domain zinc finger 
               
               
                   
                   
                   
                   
                   
                 protein 5 isfoorm 3 
               
               
                 PRKCE 
                 NM_005400 
                 chr2 
                 45879042 
                 46415129 
                 protein kinase C epsilon 
               
               
                   
                   
                   
                   
                   
                 type 
               
               
                 PRKCZ 
                 NM_001033582 
                 chr1 
                 2036154 
                 2116834 
                 protein kinase C zeta 
               
               
                   
                   
                   
                   
                   
                 type isoform 2 
               
               
                 PRUNE 
                 NM_021222 
                 chr1 
                 150980972 
                 151008189 
                 protein prune homolog 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 PTGS2 
                 NM_000963 
                 chr1 
                 186640943 
                 186649559 
                 prostaglandin G/H 
               
               
                   
                   
                   
                   
                   
                 synthase 2 precursor 
               
               
                 PTPRF 
                 NM_130440 
                 chr1 
                 43996546 
                 44089343 
                 receptor-type tyrosine- 
               
               
                   
                   
                   
                   
                   
                 protein phosphatase F 
               
               
                   
                   
                   
                   
                   
                 isoform 2 precursor 
               
               
                 PTPRZ1 
                 NM_002851 
                 chr7 
                 121513158 
                 121702090 
                 receptor-type tyrosine- 
               
               
                   
                   
                   
                   
                   
                 protein phosphatase zeta 
               
               
                   
                   
                   
                   
                   
                 isoform 1 precursor 
               
               
                 PUM1 
                 NM_014676 
                 chr1 
                 31404352 
                 31538564 
                 pumilio homolog 1 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 RAD52 
                 NM_001297419 
                 chr12 
                 1020901 
                 1099207 
                 DNA repair protein 
               
               
                   
                   
                   
                   
                   
                 RAD52 homolog 
               
               
                   
                   
                   
                   
                   
                 isoform a 
               
               
                 RAI2 
                 NM_001172743 
                 chrX 
                 17818168 
                 17879457 
                 retinoic acid-induced 
               
               
                   
                   
                   
                   
                   
                 protein 2 isoform 1 
               
               
                 RDH13 
                 NM_138412 
                 chr19 
                 55555691 
                 55580914 
                 retinol dehydrogenase 
               
               
                   
                   
                   
                   
                   
                 13 isoform 2 
               
               
                 RFWD2 
                 NM_022457 
                 chr1 
                 175913961 
                 176176380 
                 E3 ubiquitin-protein 
               
               
                   
                   
                   
                   
                   
                 ligase RFWD2 isoform 
               
               
                   
                   
                   
                   
                   
                 a 
               
               
                 RGS18 
                 NM_130782 
                 chr1 
                 192127591 
                 192154945 
                 regulator of G-protein 
               
               
                   
                   
                   
                   
                   
                 signaling 18 
               
               
                 RNF144A 
                 NM_014746 
                 chr2 
                 7057522 
                 7184309 
                 E3 ubiquitin-protein 
               
               
                   
                   
                   
                   
                   
                 ligase RNF144A 
               
               
                 SCHIP1 
                 NM_014575 
                 chr3 
                 158991035 
                 159615155 
                 schwannomin- 
               
               
                   
                   
                   
                   
                   
                 interacting protein 1 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 SERTAD2 
                 NM_014755 
                 chr2 
                 64858754 
                 64881046 
                 SERTA domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 2 
               
               
                 SGCZ 
                 NM_139167 
                 chr8 
                 13947372 
                 15095792 
                 zeta-sarcoglycan 
               
               
                 SGIP1 
                 NM_032291 
                 chr1 
                 66999824 
                 67210768 
                 SH3-containing GRB2- 
               
               
                   
                   
                   
                   
                   
                 like protein 3-interacting 
               
               
                   
                   
                   
                   
                   
                 protein 1 
               
               
                 SGPP2 
                 NM_152386 
                 chr2 
                 223289321 
                 223423617 
                 sphingosine-1- 
               
               
                   
                   
                   
                   
                   
                 phosphate phosphatase 2 
               
               
                 SH3KBP1 
                 NM_001024666 
                 chrX 
                 19552082 
                 19817917 
                 SH3 domain-containing 
               
               
                   
                   
                   
                   
                   
                 kinase-binding protein 1 
               
               
                   
                   
                   
                   
                   
                 isoform b 
               
               
                 SH3RF3 
                 NM_001099289 
                 chr2 
                 109745996 
                 110262213 
                 SH3 domain-containing 
               
               
                   
                   
                   
                   
                   
                 RING finger protein 3 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 SLC12A6 
                 NM_001042495 
                 chr15 
                 34522196 
                 34630265 
                 solute carrier family 12 
               
               
                   
                   
                   
                   
                   
                 member 6 isoform c 
               
               
                 SLC15A2 
                 NM_001145998 
                 chr3 
                 121613170 
                 121663034 
                 solute carrier family 15 
               
               
                   
                   
                   
                   
                   
                 member 2 isoform b 
               
               
                 SLC30A8 
                 NM_001172815 
                 chr8 
                 117963189 
                 118188953 
                 zinc transporter 8 
               
               
                   
                   
                   
                   
                   
                 isoform b 
               
               
                 SLC45A1 
                 NM_001080397 
                 chr1 
                 8378144 
                 8404227 
                 proton-associated sugar 
               
               
                   
                   
                   
                   
                   
                 transporter A 
               
               
                 SLC4A4 
                 NM_003759 
                 chr4 
                 72204769 
                 72437804 
                 electrogenic sodium 
               
               
                   
                   
                   
                   
                   
                 bicarbonate 
               
               
                   
                   
                   
                   
                   
                 cotransporter 1 isoform 
               
               
                   
                   
                   
                   
                   
                 2 
               
               
                 SMYD3 
                 NM_022743 
                 chr1 
                 245912641 
                 246580714 
                 histone-lysine N- 
               
               
                   
                   
                   
                   
                   
                 methyltransferase 
               
               
                   
                   
                   
                   
                   
                 SMYD3 isoform 2 
               
               
                 SNTG2 
                 NM_018968 
                 chr2 
                 946553 
                 1371384 
                 gamma-2-syntrophin 
               
               
                 SPATS2L 
                 NM_001100424 
                 chr2 
                 201170984 
                 201346986 
                 SPATS2-like protein 
               
               
                   
                   
                   
                   
                   
                 isoform b 
               
               
                 SRGAP2C 
                 NM_001271872 
                 chr1 
                 206516199 
                 206581301 
                 SLIT-ROBO Rho 
               
               
                   
                   
                   
                   
                   
                 GTPase-activating 
               
               
                   
                   
                   
                   
                   
                 protein 2C 
               
               
                 STARD9 
                 NM_020759 
                 chr15 
                 42867856 
                 43013196 
                 stAR-related lipid 
               
               
                   
                   
                   
                   
                   
                 transfer protein 9 
               
               
                 SYTL5 
                 NM_001163334 
                 chrX 
                 37892786 
                 37988073 
                 synaptotagmin-like 
               
               
                   
                   
                   
                   
                   
                 protein 5 isoform 2 
               
               
                 TBL1X 
                 NM_001139468 
                 chrX 
                 9431334 
                 9687780 
                 F-box-like/WD repeat- 
               
               
                   
                   
                   
                   
                   
                 containing protein 
               
               
                   
                   
                   
                   
                   
                 TBL1X isoform b 
               
               
                 TC2N 
                 NM_152332 
                 chr14 
                 92246095 
                 92302870 
                 tandem C2 domains 
               
               
                   
                   
                   
                   
                   
                 nuclear protein isoform 
               
               
                   
                   
                   
                   
                   
                 1 
               
               
                 TCEANC2 
                 NM_153035 
                 chr1 
                 54519273 
                 54565416 
                 transcription elongation 
               
               
                   
                   
                   
                   
                   
                 factor A N-terminal and 
               
               
                   
                   
                   
                   
                   
                 central domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 2 
               
               
                 TENM3 
                 NM_001080477 
                 chr4 
                 183245136 
                 183724177 
                 teneurin-3 
               
               
                 TEX41 
                 NR_033870 
                 chr2 
                 145425533 
                 145834291 
               
               
                 TGFBR3 
                 NM_001195683 
                 chr1 
                 92145899 
                 92351836 
                 transforming growth 
               
               
                   
                   
                   
                   
                   
                 factor beta receptor type 
               
               
                   
                   
                   
                   
                   
                 3 isoform b precursor 
               
               
                 THRAP3 
                 NM_005119 
                 chr1 
                 36690016 
                 36770957 
                 thyroid hormone 
               
               
                   
                   
                   
                   
                   
                 receptor-associated 
               
               
                   
                   
                   
                   
                   
                 protein 3 
               
               
                 TIAM1 
                 NM_003253 
                 chr21 
                 32490735 
                 32931290 
                 T-lymphoma invasion 
               
               
                   
                   
                   
                   
                   
                 and metastasis-inducing 
               
               
                   
                   
                   
                   
                   
                 protein 1 
               
               
                 TLE4 
                 NM_007005 
                 chr9 
                 82186687 
                 82341796 
                 transducin-like enhancer 
               
               
                   
                   
                   
                   
                   
                 protein 4 isoform 3 
               
               
                 TMEM236 
                 NM_001098844 
                 chr10 
                 18041226 
                 18089854 
                 transmembrane protein 
               
               
                   
                   
                   
                   
                   
                 236 
               
               
                 TNIK 
                 NM_001161561 
                 chr3 
                 170780291 
                 171178197 
                 TRAF2 and NCK- 
               
               
                   
                   
                   
                   
                   
                 interacting protein 
               
               
                   
                   
                   
                   
                   
                 kinase isoform 3 
               
               
                 TPTE2P6 
                 NR_002815 
                 chr13 
                 25154345 
                 25171812 
               
               
                 TRIM48 
                 NM_024114 
                 chr11 
                 55029657 
                 55038595 
                 tripartite motif- 
               
               
                   
                   
                   
                   
                   
                 containing protein 48 
               
               
                 TRPM8 
                 NM_024080 
                 chr2 
                 234826042 
                 234928166 
                 transient receptor 
               
               
                   
                   
                   
                   
                   
                 potential cation channel 
               
               
                   
                   
                   
                   
                   
                 subfamily M member 8 
               
               
                 TRUB2 
                 NM_015679 
                 chr9 
                 131071395 
                 131084697 
                 probable tRNA 
               
               
                   
                   
                   
                   
                   
                 pseudouridine synthase 
               
               
                   
                   
                   
                   
                   
                 2 
               
               
                 TSPAN9 
                 NM_001168320 
                 chr12 
                 3186520 
                 3395730 
                 tetraspanin-9 
               
               
                 TTC29 
                 NM_031956 
                 chr4 
                 147628178 
                 147867034 
                 tetratricopeptide repeat 
               
               
                   
                   
                   
                   
                   
                 protein 29 isoform 2 
               
               
                 TTC7B 
                 NM_001010854 
                 chr14 
                 91006931 
                 91282761 
                 tetratricopeptide repeat 
               
               
                   
                   
                   
                   
                   
                 protein 7B 
               
               
                 TTF1 
                 NM_001205296 
                 chr9 
                 135250936 
                 135282238 
                 transcription termination 
               
               
                   
                   
                   
                   
                   
                 factor 1 isoform 2 
               
               
                 VPS8 
                 NM_015303 
                 chr3 
                 184529930 
                 184770402 
                 vacuolar protein sorting- 
               
               
                   
                   
                   
                   
                   
                 associated protein 8 
               
               
                   
                   
                   
                   
                   
                 homolog isoform b 
               
               
                 WASF3 
                 NM_001291965 
                 chr13 
                 27131839 
                 27263082 
                 wiskott-Aldrich 
               
               
                   
                   
                   
                   
                   
                 syndrome protein family 
               
               
                   
                   
                   
                   
                   
                 member 3 isoform 2 
               
               
                 WBSCR16 
                 NM_001281441 
                 chr7 
                 74470621 
                 74489717 
                 Williams-Beuren 
               
               
                   
                   
                   
                   
                   
                 syndrome chromosomal 
               
               
                   
                   
                   
                   
                   
                 region 16 protein 
               
               
                   
                   
                   
                   
                   
                 isoform 3 
               
               
                 WDFY3 
                 NM_014991 
                 chr4 
                 85590692 
                 85887544 
                 WD repeat and FYVE 
               
               
                   
                   
                   
                   
                   
                 domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 3 
               
               
                 WDR17 
                 NM_181265 
                 chr4 
                 176986984 
                 177103979 
                 WD repeat-containing 
               
               
                   
                   
                   
                   
                   
                 protein 17 isoform 2 
               
               
                 WISP1 
                 NM_080838 
                 chr8 
                 134203281 
                 134243932 
                 WNT1-inducible- 
               
               
                   
                   
                   
                   
                   
                 signaling pathway 
               
               
                   
                   
                   
                   
                   
                 protein 1 isoform 2 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 XRCC5 
                 NM_021141 
                 chr2 
                 216974019 
                 217071016 
                 X-ray repair cross- 
               
               
                   
                   
                   
                   
                   
                 complementing protein 
               
               
                   
                   
                   
                   
                   
                 5 
               
               
                 YEATS2 
                 NM_018023 
                 chr3 
                 183415605 
                 183530413 
                 YEATS domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 2 
               
               
                 ZBTB41 
                 NM_194314 
                 chr1 
                 197122813 
                 197169672 
                 zinc finger and BTB 
               
               
                   
                   
                   
                   
                   
                 domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 41 
               
               
                 ZDHHC20 
                 NM_153251 
                 chr13 
                 21946709 
                 22033508 
                 probable 
               
               
                   
                   
                   
                   
                   
                 palmitoyltransferase 
               
               
                   
                   
                   
                   
                   
                 ZDHHC20 isoform 1 
               
               
                 ZNF274 
                 NM_133502 
                 chr19 
                 58694355 
                 58724928 
                 neurotrophin receptor- 
               
               
                   
                   
                   
                   
                   
                 interacting factor 
               
               
                   
                   
                   
                   
                   
                 homolog isoform c 
               
               
                 ZNF702P 
                 NR_003578 
                 chr19 
                 53471503 
                 53496784 
               
               
                 ZNF804B 
                 NM_181646 
                 chr7 
                 88388752 
                 88966346 
                 zinc finger protein 804B 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                 Genes with high expression and CN-invariant in the TCGA EOC 
               
               
                 samples (see also Table 13 for the full gene annotation). 
               
            
           
           
               
               
               
               
               
            
               
                 Symbol 
                 Probeset 
                 Median expr 
                 CV 
                 Surv. Pvalue 
               
               
                   
               
            
           
           
               
               
               
               
               
            
               
                 PDIA3 
                 208612_at 
                 10.62 
                 0.04 
                 0.20338 
               
               
                 PTPRF 
                 200636_s_at 
                 10.35 
                 0.05 
                 0.00022 
               
               
                 EIF5 
                 208705_s_at 
                 10.13 
                 0.04 
                 0.02947 
               
               
                 PUM1 
                 201166_s_at 
                 10.08 
                 0.03 
                 0.06748 
               
               
                 PTPRF 
                 200635_s_at 
                 9.88 
                 0.05 
                 0.00005 
               
               
                 NOTCH2 
                 212377_s_at 
                 9.78 
                 0.05 
                 0.05414 
               
               
                 DYRK1A 
                 209033_s_at 
                 9.86 
                 0.04 
                 0.00317 
               
               
                 XRCC5 
                 208642_s_at 
                 9.74 
                 0.04 
                 0.08567 
               
               
                 XRCC5 
                 208643_s_at 
                 9.69 
                 0.05 
                 0.00579 
               
               
                 CLIC4 
                 201560_at 
                 9.68 
                 0.05 
                 0.01722 
               
               
                 PUM1 
                 201164_s_at 
                 9.57 
                 0.04 
                 0.33393 
               
               
                 COPA 
                 208684_at 
                 9.51 
                 0.03 
                 0.20760 
               
               
                 NECAP2 
                 220731_s_at 
                 9.52 
                 0.04 
                 0.00636 
               
               
                 CUL3 
                 201371_s_at 
                 9.5 
                 0.03 
                 0.04678 
               
               
                 SPATS2L 
                 222154_s_at 
                 9.53 
                 0.06 
                 0.02196 
               
               
                 DDAH1 
                 209094_at 
                 9.5 
                 0.07 
                 0.17050 
               
               
                 DEGS1 
                 209250_at 
                 9.25 
                 0.07 
                 0.02012 
               
               
                 BRE 
                 205550_s_at 
                 9.12 
                 0.04 
                 0.02472 
               
               
                 YEATS2 
                 221203_s_at 
                 9.11 
                 0.05 
                 0.00149 
               
               
                 AMD1 
                 201197_at 
                 9.12 
                 0.04 
                 0.02027 
               
               
                 DBT 
                 205370_x_at 
                 9.1 
                 0.04 
                 0.04285 
               
               
                 MTA1 
                 211783_s_at 
                 9.06 
                 0.06 
                 0.03996 
               
               
                 PUM1 
                 201165_s_at 
                 9.08 
                 0.04 
                 0.03005 
               
               
                 FHL2 
                 202949_s_at 
                 9.03 
                 0.09 
                 0.00859 
               
               
                 NOTCH2 
                 202443_x_at 
                 9.02 
                 0.05 
                 0.01107 
               
               
                 GPBP1L1 
                 217877_s_at 
                 8.98 
                 0.03 
                 0.00688 
               
               
                 CP 
                 204846_at 
                 9.09 
                 0.14 
                 0.12168 
               
               
                 SERTAD2 
                 202657_s_at 
                 8.79 
                 0.05 
                 0.03068 
               
               
                 EHBP1 
                 212653_s_at 
                 8.64 
                 0.04 
                 0.01322 
               
               
                 GBE1 
                 203282_at 
                 8.65 
                 0.05 
                 0.17699 
               
               
                 FAT1 
                 201579_at 
                 8.77 
                 0.1 
                 0.06658 
               
               
                 AUTS2 
                 212599_at 
                 8.6 
                 0.07 
                 0.13549 
               
               
                 EIF5 
                 208706_s_at 
                 8.59 
                 0.05 
                 0.17068 
               
               
                 PRUNE 
                 209586_s_at 
                 8.45 
                 0.05 
                 0.13525 
               
               
                 RAI2 
                 219440_at 
                 8.49 
                 0.09 
                 0.10687 
               
               
                 EIF5 
                 208708_x_at 
                 8.44 
                 0.06 
                 0.00692 
               
               
                 PTPRF 
                 200637_s_at 
                 8.37 
                 0.06 
                 0.01045 
               
               
                 SERTAD2 
                 202656_s_at 
                 8.35 
                 0.05 
                 0.04363 
               
               
                 FHL1 
                 201540_at 
                 8.27 
                 0.12 
                 0.09021 
               
               
                 TBL1X 
                 213400_s_at 
                 8.38 
                 0.09 
                 0.04973 
               
               
                 NUP133 
                 202184_s_at 
                 8.36 
                 0.04 
                 0.00319 
               
               
                 NT5C2 
                 209155_s_at 
                 8.28 
                 0.05 
                 0.32412 
               
               
                 TGFBR3 
                 204731_at 
                 8.15 
                 0.08 
                 0.01399 
               
               
                 VPS8 
                 209553_at 
                 8.17 
                 0.05 
                 0.02758 
               
               
                 PARN 
                 203905_at 
                 8.14 
                 0.05 
                 0.07753 
               
               
                 DAPK1 
                 203139_at 
                 8.1 
                 0.07 
                 0.07083 
               
               
                 ERBB4 
                 214053_at 
                 8.19 
                 0.13 
                 0.08732 
               
               
                 TIAM1 
                 213135_at 
                 8.1 
                 0.07 
                 0.12098 
               
               
                 SCHIP1 
                 204030_s_at 
                 8.07 
                 0.09 
                 0.08119 
               
               
                 MTR 
                 203774_at 
                 8.06 
                 0.06 
                 0.12443 
               
               
                 SMYD3 
                 218788_s_at 
                 8.11 
                 0.06 
                 0.02778 
               
               
                 ZNF274 
                 204937_s_at 
                 8.05 
                 0.05 
                 0.05063 
               
               
                 DEGS1 
                 207431_s_at 
                 8.03 
                 0.07 
                 0.00519 
               
               
                 BRE 
                 212645_x_at 
                 8.01 
                 0.04 
                 0.07055 
               
               
                 BRE 
                 211566_x_at 
                 8.01 
                 0.04 
                 0.11351 
               
               
                 KIAA0430 
                 202386_s_at 
                 8.01 
                 0.04 
                 0.00140 
               
               
                 TTF1 
                 204771_s_at 
                 7.99 
                 0.04 
                 0.27136 
               
               
                 ENPP2 
                 209392_at 
                 7.93 
                 0.09 
                 0.00721 
               
               
                 AGAP1 
                 204066_s_at 
                 7.99 
                 0.06 
                 0.04297 
               
               
                 PRKCZ 
                 202178_at 
                 7.95 
                 0.06 
                 0.11192 
               
               
                 FAHD2A 
                 222056_s_at 
                 7.89 
                 0.05 
                 0.03631 
               
               
                 AMD1 
                 201196_s_at 
                 7.85 
                 0.05 
                 0.07653 
               
               
                 NOTCH2 
                 210756_s_at 
                 7.81 
                 0.04 
                 0.12557 
               
               
                 MORC3 
                 213000_at 
                 7.81 
                 0.04 
                 0.02729 
               
               
                 CHST15 
                 203066_at 
                 7.82 
                 0.1 
                 0.00896 
               
               
                 RNF144A 
                 204040_at 
                 7.75 
                 0.08 
                 0.05543 
               
               
                 ASCC3 
                 212815_at 
                 7.75 
                 0.05 
                 0.10970 
               
               
                 ACYP2 
                 206833_s_at 
                 7.69 
                 0.07 
                 0.00031 
               
               
                 EIF5 
                 208290_s_at 
                 7.65 
                 0.06 
                 0.01586 
               
               
                 CLMN 
                 221042_s_at 
                 7.63 
                 0.06 
                 0.30167 
               
               
                 FAHD2A 
                 218504_at 
                 7.59 
                 0.05 
                 0.15978 
               
               
                 LEF1 
                 221558_s_at 
                 7.49 
                 0.12 
                 0.01963 
               
               
                 CLASP1 
                 212752_at 
                 7.57 
                 0.04 
                 0.20654 
               
               
                 WASF3 
                 204042_at 
                 7.6 
                 0.09 
                 0.02224 
               
               
                 TSPAN9 
                 220968_s_at 
                 7.58 
                 0.05 
                 0.00037 
               
               
                 TBL1X 
                 201867_s_at 
                 7.54 
                 0.07 
                 0.02455 
               
               
                 CLIC4 
                 221881_s_at 
                 7.56 
                 0.06 
                 0.02110 
               
               
                 PRUNE 
                 210988_s_at 
                 7.46 
                 0.04 
                 0.23481 
               
               
                 SLC15A2 
                 205316_at 
                 7.35 
                 0.1 
                 0.01251 
               
               
                 WDFY3 
                 212602_at 
                 7.44 
                 0.05 
                 0.12013 
               
               
                 RAB11FIP1 
                 219681_s_at 
                 7.33 
                 0.08 
                 0.07390 
               
               
                 WBSCR16 
                 221247_s_at 
                 7.39 
                 0.04 
                 0.03208 
               
               
                 EHBP1 
                 212650_at 
                 7.37 
                 0.03 
                 0.01359 
               
               
                 NMD3 
                 218036_x_at 
                 7.35 
                 0.04 
                 0.09489 
               
               
                 POU2F1 
                 206789_s_at 
                 7.38 
                 0.04 
                 0.06434 
               
               
                 BMPR2 
                 210214_s_at 
                 7.33 
                 0.05 
                 0.00025 
               
               
                 ATXN7 
                 204516_at 
                 7.33 
                 0.05 
                 0.02880 
               
               
                 PTPRF 
                 215066_at 
                 7.26 
                 0.03 
                 0.04876 
               
               
                 FHIT 
                 206492_at 
                 7.2 
                 0.07 
                 0.19039 
               
               
                 EPHB2 
                 211165_x_at 
                 7.18 
                 0.06 
                 0.01610 
               
               
                 FCGR2A 
                 203561_at 
                 7.18 
                 0.1 
                 0.00242 
               
               
                 ARHGAP10 
                 219431_at 
                 7.19 
                 0.04 
                 0.19969 
               
               
                 PHTF1 
                 210191_s_at 
                 7.17 
                 0.04 
                 0.00273 
               
               
                 ENPP2 
                 210839_s_at 
                 7.08 
                 0.07 
                 0.03070 
               
               
                 FHL1 
                 210299_s_at 
                 7.01 
                 0.12 
                 0.06449 
               
               
                 IL15 
                 205992_s_at 
                 7.13 
                 0.12 
                 0.07816 
               
               
                 H6PD 
                 221892_at 
                 7.14 
                 0.05 
                 0.01491 
               
               
                 WDFY3 
                 212606_at 
                 7.14 
                 0.04 
                 0.04054 
               
               
                 NLGN4X 
                 221933_at 
                 6.97 
                 0.1 
                 0.02676 
               
               
                 ABHD5 
                 218739_at 
                 7.13 
                 0.04 
                 0.06548 
               
               
                 CLIC4 
                 201559_s_at 
                 7.13 
                 0.05 
                 0.00946 
               
               
                 CLMN 
                 213839_at 
                 7.08 
                 0.07 
                 0.07973 
               
               
                 CHL1 
                 204591_at 
                 6.99 
                 0.15 
                 0.07302 
               
               
                 EPHB2 
                 209588_at 
                 7.09 
                 0.05 
                 0.15543 
               
               
                 MAN1A1 
                 221760_at 
                 7.12 
                 0.11 
                 0.05231 
               
               
                 BMPR2 
                 209920_at 
                 7.11 
                 0.05 
                 0.00521 
               
               
                 EPHB2 
                 210651_s_at 
                 7.08 
                 0.03 
                 0.03742 
               
               
                 FGF12 
                 214589_at 
                 7.1 
                 0.02 
                 0.07807 
               
               
                 FGGY 
                 219718_at 
                 7.04 
                 0.05 
                 0.04990 
               
               
                 TLE4 
                 204872_at 
                 7.01 
                 0.09 
                 0.14776 
               
               
                 FUT9 
                 216185_at 
                 7.07 
                 0.02 
                 0.02171 
               
               
                 EPHB2 
                 209589_s_at 
                 7.01 
                 0.06 
                 0.06130 
               
               
                 ASAP1 
                 221039_s_at 
                 7.01 
                 0.05 
                 0.00590 
               
               
                 IL5RA 
                 210744_s_at 
                 7.05 
                 0.02 
                 0.03824 
               
               
                 EFHC2 
                 220591_s_at 
                 6.94 
                 0.08 
                 0.02003 
               
               
                 TTF1 
                 204772_s_at 
                 7.03 
                 0.03 
                 0.00623 
               
               
                 ATF7IP2 
                 219870_at 
                 7.03 
                 0.04 
                 0.09257 
               
               
                 ANK2 
                 202920_at 
                 6.88 
                 0.11 
                 0.13741 
               
               
                 MFAP3L 
                 210493_s_at 
                 7.02 
                 0.02 
                 0.18480 
               
               
                 GOLIM4 
                 204324_s_at 
                 7 
                 0.05 
                 0.19382 
               
               
                 EHD3 
                 218935_at 
                 7 
                 0.05 
                 0.15127 
               
               
                 DAB1 
                 220611_at 
                 7.01 
                 0.02 
                 0.01393 
               
               
                 DBT 
                 205369_x_at 
                 7 
                 0.04 
                 0.03095 
               
               
                 FHL1 
                 214505_s_at 
                 6.86 
                 0.09 
                 0.01801 
               
               
                 TGFBRAP1 
                 205210_at 
                 6.95 
                 0.03 
                 0.00127 
               
               
                 PHTF1 
                 205702_at 
                 6.91 
                 0.04 
                 0.00146 
               
               
                 TIAM1 
                 206409_at 
                 6.9 
                 0.03 
                 0.28210 
               
               
                 LDB2 
                 206481_s_at 
                 6.86 
                 0.05 
                 0.07078 
               
               
                 ABHD5 
                 213935_at 
                 6.89 
                 0.03 
                 0.04094 
               
               
                 CACNA2D1 
                 207050_at 
                 6.9 
                 0.02 
                 0.29669 
               
               
                 LYST 
                 210943_s_at 
                 6.86 
                 0.04 
                 0.14418 
               
               
                 RAD52 
                 205647_at 
                 6.87 
                 0.03 
                 0.02273 
               
               
                 CUL3 
                 201370_s_at 
                 6.87 
                 0.07 
                 0.03293 
               
               
                 LEF1 
                 210948_s_at 
                 6.77 
                 0.09 
                 0.07087 
               
               
                 HHAT 
                 219687_at 
                 6.84 
                 0.06 
                 0.00428 
               
               
                 EPB41 
                 207793_s_at 
                 6.87 
                 0.02 
                 0.01335 
               
               
                 ATAD2B 
                 213387_at 
                 6.83 
                 0.03 
                 0.01759 
               
               
                 DBT 
                 205371_s_at 
                 6.82 
                 0.04 
                 0.06851 
               
               
                 GTF2F2 
                 209595_at 
                 6.8 
                 0.03 
                 0.01296 
               
               
                 ESRRG 
                 207981_s_at 
                 6.73 
                 0.07 
                 0.09335 
               
               
                 FHL1 
                 210298_x_at 
                 6.67 
                 0.09 
                 0.00971 
               
               
                 KIT 
                 205051_s_at 
                 6.73 
                 0.06 
                 0.00802 
               
               
                 DNM3 
                 209839_at 
                 6.72 
                 0.05 
                 0.01017 
               
               
                 PCDH7 
                 205535_s_at 
                 6.78 
                 0.03 
                 0.01285 
               
               
                 NEIL3 
                 219502_at 
                 6.76 
                 0.03 
                 0.09424 
               
               
                 C1orf21 
                 221272_s_at 
                 6.75 
                 0.03 
                 0.02970 
               
               
                 MFAP3L 
                 205442_at 
                 6.68 
                 0.06 
                 0.15633 
               
               
                 GLI2 
                 208057_s_at 
                 6.76 
                 0.04 
                 0.03577 
               
               
                 PLEKHA2 
                 217677_at 
                 6.74 
                 0.03 
                 0.04937 
               
               
                 FAM49A 
                 208092_s_at 
                 6.69 
                 0.05 
                 0.01330 
               
               
                 COPA 
                 214336_s_at 
                 6.75 
                 0.04 
                 0.00146 
               
               
                 DEPDC1 
                 220295_x_at 
                 6.7 
                 0.07 
                 0.05928 
               
               
                 WDFY3 
                 212598_at 
                 6.73 
                 0.02 
                 0.00706 
               
               
                 TBL1X 
                 201868_s_at 
                 6.69 
                 0.05 
                 0.02552 
               
               
                 ERBB4 
                 206794_at 
                 6.67 
                 0.04 
                 0.05339 
               
               
                 HYAL3 
                 211728_s_at 
                 6.67 
                 0.05 
                 0.05147 
               
               
                 BTNL8 
                 220421_at 
                 6.68 
                 0.04 
                 0.04656 
               
               
                 HRG 
                 31835_at 
                 6.69 
                 0.02 
                 0.02679 
               
               
                 TBL1X 
                 201869_s_at 
                 6.66 
                 0.05 
                 0.05697 
               
               
                 KCNAB1 
                 210079_x_at 
                 6.69 
                 0.02 
                 0.02286 
               
               
                 LYST 
                 203518_at 
                 6.66 
                 0.04 
                 0.00863 
               
               
                 PDE2A 
                 204134_at 
                 6.64 
                 0.03 
                 0.01786 
               
               
                 NOTCH2 
                 202445_s_at 
                 6.63 
                 0.04 
                 0.00017 
               
               
                 SP4 
                 206663_at 
                 6.66 
                 0.02 
                 0.06132 
               
               
                 TNIK 
                 213107_at 
                 6.61 
                 0.05 
                 0.00333 
               
               
                 SLC15A2 
                 205317_s_at 
                 6.56 
                 0.05 
                 0.02679 
               
               
                 ESRRG 
                 209966_x_at 
                 6.57 
                 0.07 
                 0.00368 
               
               
                 LAMC3 
                 219407_s_at 
                 6.58 
                 0.06 
                 0.02266 
               
               
                 PCDH7 
                 210273_at 
                 6.58 
                 0.06 
                 0.03610 
               
               
                 MTA1 
                 202247_s_at 
                 6.64 
                 0.03 
                 0.05778 
               
               
                 DAPK1 
                 211214_s_at 
                 6.63 
                 0.02 
                 0.07588 
               
               
                 AFF3 
                 205735_s_at 
                 6.64 
                 0.02 
                 0.06791 
               
               
                 HS3ST1 
                 213991_s_at 
                 6.62 
                 0.03 
                 0.08849 
               
               
                 PHTF1 
                 215285_s_at 
                 6.6 
                 0.04 
                 0.00014 
               
               
                 IL15 
                 217371_s_at 
                 6.55 
                 0.07 
                 0.00521 
               
               
                 HS3ST1 
                 205466_s_at 
                 6.58 
                 0.07 
                 0.06365 
               
               
                 PCDH7 
                 205534_at 
                 6.47 
                 0.1 
                 0.04277 
               
               
                 LPHN3 
                 209867_s_at 
                 6.56 
                 0.04 
                 0.00607 
               
               
                 PCOLCE2 
                 219295_s_at 
                 6.53 
                 0.05 
                 0.03009 
               
               
                 FHL1 
                 201539_s_at 
                 6.48 
                 0.07 
                 0.00691 
               
               
                 ABHD5 
                 213805_at 
                 6.56 
                 0.02 
                 0.03415 
               
               
                 CAMTA1 
                 213268_at 
                 6.53 
                 0.05 
                 0.04646 
               
               
                 CASQ2 
                 207317_s_at 
                 6.53 
                 0.03 
                 0.16039 
               
               
                 RAD52 
                 211904_x_at 
                 6.57 
                 0.03 
                 0.13310 
               
               
                 ATXN7 
                 209964_s_at 
                 6.55 
                 0.02 
                 0.06355 
               
               
                 SLC4A4 
                 210739_x_at 
                 6.55 
                 0.02 
                 0.04069 
               
               
                 GRM8 
                 216256_at 
                 6.55 
                 0.01 
                 0.04053 
               
               
                 THRAP3 
                 217847_s_at 
                 6.55 
                 0.02 
                 0.00935 
               
               
                 HTR4 
                 207578_s_at 
                 6.54 
                 0.01 
                 0.21199 
               
               
                 MAN1A1 
                 208116_s_at 
                 6.52 
                 0.04 
                 0.04868 
               
               
                 TRPM8 
                 220226_at 
                 6.53 
                 0.02 
                 0.12609 
               
               
                 PRKCE 
                 206248_at 
                 6.52 
                 0.02 
                 0.03066 
               
               
                 TBL1X 
                 213401_s_at 
                 6.51 
                 0.03 
                 0.12794 
               
               
                 EIF5 
                 208707_at 
                 6.49 
                 0.03 
                 0.02177 
               
               
                 TNIK 
                 213109_at 
                 6.42 
                 0.07 
                 0.00566 
               
               
                 PRUNE 
                 209599_s_at 
                 6.51 
                 0.03 
                 0.10137 
               
               
                 TLE4 
                 214688_at 
                 6.48 
                 0.04 
                 0.21103 
               
               
                 CUL3 
                 201372_s_at 
                 6.51 
                 0.03 
                 0.07651 
               
               
                 DYRK1A 
                 211541_s_at 
                 6.5 
                 0.03 
                 0.02780 
               
               
                 BATF3 
                 220358_at 
                 6.48 
                 0.02 
                 0.11090 
               
               
                 NRP2 
                 214632_at 
                 6.47 
                 0.04 
                 0.13341 
               
               
                 SLC4A4 
                 203908_at 
                 6.43 
                 0.06 
                 0.10032 
               
               
                 SLC12A6 
                 220740_s_at 
                 6.5 
                 0.02 
                 0.09519 
               
               
                 FGF12 
                 207501_s_at 
                 6.44 
                 0.03 
                 0.07473 
               
               
                 PTGS2 
                 204748_at 
                 6.35 
                 0.08 
                 0.10158 
               
               
                 GLI2 
                 207034_s_at 
                 6.43 
                 0.03 
                 0.00107 
               
               
                 KCNAB1 
                 210078_s_at 
                 6.44 
                 0.04 
                 0.16319 
               
               
                 TSPAN9 
                 205665_at 
                 6.42 
                 0.03 
                 0.05611 
               
               
                 ZNF702P 
                 206557_at 
                 6.41 
                 0.04 
                 0.05041 
               
               
                 NRP2 
                 210841_s_at 
                 6.42 
                 0.02 
                 0.24581 
               
               
                 ANK2 
                 202921_s_at 
                 6.41 
                 0.02 
                 0.13182 
               
               
                 CACNB2 
                 207776_s_at 
                 6.43 
                 0.01 
                 0.28364 
               
               
                 GAP43 
                 216963_s_at 
                 6.42 
                 0.02 
                 0.00607 
               
               
                 PTPRZ1 
                 204469_at 
                 6.41 
                 0.04 
                 0.00006 
               
               
                 RAD52 
                 210630_s_at 
                 6.39 
                 0.03 
                 0.00192 
               
               
                 FAM49A 
                 209683_at 
                 6.38 
                 0.04 
                 0.00367 
               
               
                 TNIK 
                 211828_s_at 
                 6.34 
                 0.05 
                 0.12912 
               
               
                 IL5RA 
                 211516_at 
                 6.38 
                 0.03 
                 0.03421 
               
               
                 CACNB2 
                 213714_at 
                 6.38 
                 0.02 
                 0.00153 
               
               
                 LPHN3 
                 209866_s_at 
                 6.25 
                 0.07 
                 0.00313 
               
               
                 TEC 
                 206301_at 
                 6.37 
                 0.02 
                 0.01093 
               
               
                 GAP43 
                 204471_at 
                 6.35 
                 0.03 
                 0.03357 
               
               
                 PRDM5 
                 220792_at 
                 6.37 
                 0.02 
                 0.05073 
               
               
                 KCNAB1 
                 208213_s_at 
                 6.37 
                 0.01 
                 0.14705 
               
               
                 ARSE 
                 205894_at 
                 6.33 
                 0.03 
                 0.08378 
               
               
                 CCDC88A 
                 219387_at 
                 6.31 
                 0.05 
                 0.26252 
               
               
                 IL5RA 
                 207902_at 
                 6.34 
                 0.01 
                 0.04565 
               
               
                 ANK2 
                 216195_at 
                 6.34 
                 0.02 
                 0.09666 
               
               
                 TLE4 
                 216997_x_at 
                 6.34 
                 0.02 
                 0.02096 
               
               
                 ERC2 
                 213938_at 
                 6.31 
                 0.03 
                 0.14336 
               
               
                 HS3ST1 
                 205465_x_at 
                 6.34 
                 0.02 
                 0.04735 
               
               
                 SLC4A4 
                 211494_s_at 
                 6.31 
                 0.02 
                 0.04845 
               
               
                 CACNB2 
                 215365_at 
                 6.32 
                 0.01 
                 0.04082 
               
               
                 COPA 
                 214337_at 
                 6.32 
                 0.01 
                 0.11916 
               
               
                 PDZK1 
                 205380_at 
                 6.22 
                 0.06 
                 0.04122 
               
               
                 CCDC88A 
                 221078_s_at 
                 6.31 
                 0.02 
                 0.06450 
               
               
                 HTR4 
                 216939_s_at 
                 6.31 
                 0.02 
                 0.00770 
               
               
                 HRG 
                 206226_at 
                 6.3 
                 0.02 
                 0.01240 
               
               
                 NRP2 
                 211844_s_at 
                 6.29 
                 0.03 
                 0.00660 
               
               
                 WISP1 
                 206796_at 
                 6.25 
                 0.04 
                 0.00666 
               
               
                 LYST 
                 215415_s_at 
                 6.29 
                 0.01 
                 0.00385 
               
               
                 H6PD 
                 206933_s_at 
                 6.28 
                 0.01 
                 0.00046 
               
               
                 NTNG1 
                 206713_at 
                 6.28 
                 0.01 
                 0.12339 
               
               
                 WISP1 
                 211312_s_at 
                 6.28 
                 0.01 
                 0.01658 
               
               
                 NRXN1 
                 209914_s_at 
                 6.28 
                 0.01 
                 0.14478 
               
               
                 MCTP1 
                 220122_at 
                 6.23 
                 0.04 
                 0.04156 
               
               
                 IL5RA 
                 211517_s_at 
                 6.26 
                 0.02 
                 0.29333 
               
               
                 MFAP3L 
                 210843_s_at 
                 6.26 
                 0.02 
                 0.01571 
               
               
                 PRDM16 
                 220928_s_at 
                 6.26 
                 0.02 
                 0.00062 
               
               
                 LEF1 
                 221557_s_at 
                 6.26 
                 0.01 
                 0.11284 
               
               
                 NRXN1 
                 216096_s_at 
                 6.24 
                 0.03 
                 0.00120 
               
               
                 SLC4A4 
                 210738_s_at 
                 6.24 
                 0.03 
                 0.15578 
               
               
                 HTR4 
                 207577_at 
                 6.26 
                 0.01 
                 0.26027 
               
               
                 TRIM48 
                 220534_at 
                 6.25 
                 0.02 
                 0.11769 
               
               
                 DBT 
                 211196_at 
                 6.25 
                 0.01 
                 0.02950 
               
               
                 GRM8 
                 216992_s_at 
                 6.25 
                 0.02 
                 0.00285 
               
               
                 SPATS2L 
                 215617_at 
                 6.23 
                 0.03 
                 0.02000 
               
               
                 ABCB4 
                 207819_s_at 
                 6.24 
                 0.02 
                 0.01195 
               
               
                 AFF3 
                 205734_s_at 
                 6.24 
                 0.01 
                 0.08057 
               
               
                 NRP2 
                 210842_at 
                 6.22 
                 0.02 
                 0.17198 
               
               
                 KCNAB1 
                 210471_s_at 
                 6.2 
                 0.02 
                 0.01435 
               
               
                 MFAP3L 
                 210492_at 
                 6.19 
                 0.02 
                 0.01254 
               
               
                 EFHC2 
                 220523_at 
                 6.2 
                 0.01 
                 0.01661 
               
               
                 EPB41 
                 214530_x_at 
                 6.2 
                 0.01 
                 0.00585 
               
               
                 GRM8 
                 216255_s_at 
                 6.2 
                 0.01 
                 0.02002 
               
               
                 DYRK1A 
                 211079_s_at 
                 6.19 
                 0.01 
                 0.11899 
               
               
                 FUT9 
                 207696_at 
                 6.14 
                 0.01 
                 0.05224 
               
               
                 FUT9 
                 214046_at 
                 6.13 
                 0.03 
                 0.06542 
               
               
                 LRCH1 
                 214936_at 
                 6.13 
                 0.02 
                 0.07138 
               
               
                 NRXN1 
                 209915_s_at 
                 6.12 
                 0.01 
                 0.16486 
               
               
                 LRP1B 
                 219643_at 
                 6.06 
                 0.04 
                 0.02452 
               
               
                 SNTG2 
                 220487_at 
                 6.08 
                 0.01 
                 0.12133 
               
               
                 PDE6C 
                 211093_at 
                 6.07 
                 0.01 
                 0.03750 
               
               
                 PCDH7 
                 210941_at 
                 6.03 
                 0.03 
                 0.04561 
               
               
                 CASC5 
                 220247_at 
                 6 
                 0.01 
                 0.11084 
               
               
                 DPPA4 
                 219651_at 
                 5.95 
                 0.04 
                 0.00008 
               
               
                   
               
               
                 Median expr = median log expression value across the samples; CV = coefficient of variation of the log expression values; Surv. P value = survival p-value. 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 3 
               
             
            
               
                   
               
               
                 Genes with high expression in GSE9899 and CN-invariant in TCGA 
               
               
                 EOC samples (see also Table 14 for the full gene annotation). 
               
            
           
           
               
               
               
               
               
            
               
                 Symbol 
                 Probeset 
                 Median expr 
                 CV 
                 Surv. Pvalue 
               
               
                   
               
            
           
           
               
               
               
               
               
            
               
                 DBT 
                 205370_x_at 
                 12.25 
                 0.02 
                 0.02040 
               
               
                 NOTCH2 
                 202443_x_at 
                 11.46 
                 0.04 
                 0.17253 
               
               
                 PDIA3 
                 208612_at 
                 11.24 
                 0.04 
                 0.02038 
               
               
                 PUM1 
                 201166_s_at 
                 11.21 
                 0.03 
                 0.03512 
               
               
                 XRCC5 
                 208642_s_at 
                 11.09 
                 0.03 
                 0.22739 
               
               
                 PTPRF 
                 200636_s_at 
                 11.06 
                 0.05 
                 0.24272 
               
               
                 NOTCH2 
                 212377_s_at 
                 10.86 
                 0.04 
                 0.02659 
               
               
                 CLIC4 
                 201560_at 
                 10.77 
                 0.05 
                 0.00009 
               
               
                 SPATS2L 
                 222154_s_at 
                 10.68 
                 0.06 
                 0.01236 
               
               
                 COPA 
                 208684_at 
                 10.66 
                 0.03 
                 0.00455 
               
               
                 EIF5 
                 208705_s_at 
                 10.65 
                 0.04 
                 0.06987 
               
               
                 PUM1 
                 201164_s_at 
                 10.64 
                 0.03 
                 0.02840 
               
               
                 XRCC5 
                 208643_s_at 
                 10.62 
                 0.04 
                 0.06877 
               
               
                 CUL3 
                 201371_s_at 
                 10.46 
                 0.03 
                 0.03970 
               
               
                 CP 
                 204846_at 
                 10.36 
                 0.13 
                 0.02147 
               
               
                 DYRK1A 
                 209033_s_at 
                 10.34 
                 0.03 
                 0.12664 
               
               
                 FHL2 
                 202949_s_at 
                 10.25 
                 0.08 
                 0.11226 
               
               
                 PUM1 
                 201165_s_at 
                 10.17 
                 0.04 
                 0.07656 
               
               
                 AUTS2 
                 212599_at 
                 9.99 
                 0.06 
                 0.06148 
               
               
                 NT5C2 
                 209155_s_at 
                 9.95 
                 0.04 
                 0.00538 
               
               
                 EIF5 
                 208706_s_at 
                 9.93 
                 0.04 
                 0.06033 
               
               
                 DDAH1 
                 209094_at 
                 9.92 
                 0.06 
                 0.01562 
               
               
                 DEGS1 
                 209250_at 
                 9.88 
                 0.06 
                 0.00232 
               
               
                 PTPRF 
                 200635_s_at 
                 9.85 
                 0.06 
                 0.06567 
               
               
                 AMD1 
                 201197_at 
                 9.8 
                 0.04 
                 0.05652 
               
               
                 GPBP1L1 
                 217877_s_at 
                 9.76 
                 0.03 
                 0.04268 
               
               
                 YEATS2 
                 221203_s_at 
                 9.69 
                 0.05 
                 0.00233 
               
               
                 GLI2 
                 208057_s_at 
                 9.64 
                 0.05 
                 0.30579 
               
               
                 FAT1 
                 201579_at 
                 9.58 
                 0.1 
                 0.00624 
               
               
                 FHL1 
                 201540_at 
                 9.58 
                 0.1 
                 0.03419 
               
               
                 PARN 
                 203905_at 
                 9.55 
                 0.03 
                 0.27358 
               
               
                 NUP133 
                 202184_s_at 
                 9.52 
                 0.04 
                 0.18819 
               
               
                 NECAP2 
                 220731_s_at 
                 9.51 
                 0.04 
                 0.01493 
               
               
                 SERTAD2 
                 202657_s_at 
                 9.49 
                 0.05 
                 0.00899 
               
               
                 ATXN7 
                 204516_at 
                 9.47 
                 0.04 
                 0.01148 
               
               
                 CHST15 
                 203066_at 
                 9.47 
                 0.08 
                 0.00870 
               
               
                 EIF5 
                 208708_x_at 
                 9.46 
                 0.04 
                 0.04619 
               
               
                 MORC3 
                 213000_at 
                 9.46 
                 0.04 
                 0.01305 
               
               
                 GBE1 
                 203282_at 
                 9.45 
                 0.05 
                 0.03451 
               
               
                 BRE 
                 205550_s_at 
                 9.34 
                 0.04 
                 0.18017 
               
               
                 LEF1 
                 221558_s_at 
                 9.32 
                 0.1 
                 0.06360 
               
               
                 SERTAD2 
                 202656_s_at 
                 9.3 
                 0.05 
                 0.01998 
               
               
                 RAI2 
                 219440_at 
                 9.24 
                 0.09 
                 0.00090 
               
               
                 MTA1 
                 211783_s_at 
                 9.21 
                 0.05 
                 0.06242 
               
               
                 DAPK1 
                 203139_at 
                 9.17 
                 0.06 
                 0.11341 
               
               
                 PRUNE 
                 209586_s_at 
                 9.17 
                 0.05 
                 0.00825 
               
               
                 DEGS1 
                 207431_s_at 
                 9.17 
                 0.06 
                 0.01518 
               
               
                 RNF144A 
                 204040_at 
                 9.08 
                 0.07 
                 0.04822 
               
               
                 PTPRF 
                 215066_at 
                 9.04 
                 0.04 
                 0.05418 
               
               
                 SMYD3 
                 218788_s_at 
                 9.04 
                 0.06 
                 0.00233 
               
               
                 EHBP1 
                 212653_s_at 
                 9.03 
                 0.04 
                 0.00489 
               
               
                 TBL1X 
                 213400_s_at 
                 9.03 
                 0.06 
                 0.06571 
               
               
                 MAN1A1 
                 221760_at 
                 9.02 
                 0.1 
                 0.04635 
               
               
                 NOTCH2 
                 210756_s_at 
                 9.01 
                 0.05 
                 0.03153 
               
               
                 PTPRF 
                 200637_s_at 
                 9.01 
                 0.07 
                 0.09062 
               
               
                 WBSCR16 
                 221247_s_at 
                 9 
                 0.03 
                 0.00512 
               
               
                 tabular VPS8 
                 209553_at 
                 8.96 
                 0.04 
                 0.01131 
               
               
                 BRE 
                 212645_x_at 
                 8.95 
                 0.03 
                 0.29607 
               
               
                 KIAA0430 
                 202386_s_at 
                 8.89 
                 0.04 
                 0.08524 
               
               
                 BRE 
                 211566_x_at 
                 8.89 
                 0.04 
                 0.22934 
               
               
                 TTF1 
                 204771_s_at 
                 8.86 
                 0.05 
                 0.04547 
               
               
                 MTR 
                 203774_at 
                 8.82 
                 0.05 
                 0.13164 
               
               
                 NMD3 
                 218036_x_at 
                 8.81 
                 0.04 
                 0.17399 
               
               
                 CUL3 
                 201370_s_at 
                 8.81 
                 0.05 
                 0.09902 
               
               
                 EIF5 
                 208290_s_at 
                 8.81 
                 0.05 
                 0.05245 
               
               
                 TSPAN9 
                 220968_s_at 
                 8.79 
                 0.04 
                 0.00043 
               
               
                 FCGR2A 
                 203561_at 
                 8.76 
                 0.09 
                 0.15164 
               
               
                 TIAM1 
                 213135_at 
                 8.75 
                 0.07 
                 0.02124 
               
               
                 AGAP1 
                 204066_s_at 
                 8.74 
                 0.06 
                 0.01199 
               
               
                 ENPP2 
                 209392_at 
                 8.73 
                 0.09 
                 0.01476 
               
               
                 AMD1 
                 201196_s_at 
                 8.68 
                 0.04 
                 0.06565 
               
               
                 FAHD2A 
                 222056_s_at 
                 8.68 
                 0.05 
                 0.08837 
               
               
                 ZNF274 
                 204937_s_at 
                 8.67 
                 0.05 
                 0.14136 
               
               
                 ERBB4 
                 214053_at 
                 8.6 
                 0.14 
                 0.01026 
               
               
                 FAHD2A 
                 218504_at 
                 8.59 
                 0.03 
                 0.01900 
               
               
                 ASCC3 
                 212815_at 
                 8.56 
                 0.05 
                 0.18424 
               
               
                 ATXN7 
                 209964_s_at 
                 8.54 
                 0.05 
                 0.01107 
               
               
                 ASAP1 
                 221039_s_at 
                 8.53 
                 0.05 
                 0.11827 
               
               
                 CLASP1 
                 212752_at 
                 8.47 
                 0.03 
                 0.00053 
               
               
                 HRG 
                 31835_at 
                 8.43 
                 0.03 
                 0.07209 
               
               
                 CLMN 
                 213839_at 
                 8.42 
                 0.06 
                 0.00381 
               
               
                 TLE4 
                 204872_at 
                 8.29 
                 0.1 
                 0.05946 
               
               
                 H6PD 
                 221892_at 
                 8.28 
                 0.05 
                 0.01582 
               
               
                 PRKCZ 
                 202178_at 
                 8.28 
                 0.05 
                 0.09564 
               
               
                 SCHIP1 
                 204030_s_at 
                 8.24 
                 0.08 
                 0.00021 
               
               
                 EPHB2 
                 209588_at 
                 8.21 
                 0.03 
                 0.00274 
               
               
                 WDFY3 
                 212606_at 
                 8.21 
                 0.04 
                 0.00012 
               
               
                 TIAM1 
                 206409_at 
                 8.18 
                 0.04 
                 0.07169 
               
               
                 PRUNE 
                 210988_s_at 
                 8.17 
                 0.04 
                 0.02233 
               
               
                 CLMN 
                 221042_s_at 
                 8.15 
                 0.06 
                 0.04387 
               
               
                 POU2F1 
                 206789_s_at 
                 8.13 
                 0.03 
                 0.03589 
               
               
                 TGFBR3 
                 204731_at 
                 8.12 
                 0.09 
                 0.02006 
               
               
                 WASF3 
                 204042_at 
                 8.1 
                 0.09 
                 0.00186 
               
               
                 ENPP2 
                 210839_s_at 
                 8.09 
                 0.08 
                 0.01530 
               
               
                 EPHB2 
                 210651_s_at 
                 8.06 
                 0.03 
                 0.00118 
               
               
                 CLIC4 
                 201559_s_at 
                 8.06 
                 0.07 
                 0.10860 
               
               
                 RAB11FIP1 
                 219681_s_at 
                 8.03 
                 0.09 
                 0.08002 
               
               
                 FHL1 
                 214505_s_at 
                 8.02 
                 0.06 
                 0.00468 
               
               
                 CHL1 
                 204591_at 
                 8.01 
                 0.15 
                 0.07569 
               
               
                 WDFY3 
                 212602_at 
                 8 
                 0.04 
                 0.31880 
               
               
                 CLIC4 
                 221881_s_at 
                 8 
                 0.06 
                 0.04131 
               
               
                 TBL1X 
                 201869_s_at 
                 7.96 
                 0.05 
                 0.03666 
               
               
                 EPHB2 
                 209589_s_at 
                 7.93 
                 0.06 
                 0.00015 
               
               
                 AXF7IP2 
                 219870_at 
                 7.93 
                 0.05 
                 0.06342 
               
               
                 ACYP2 
                 206833_s_at 
                 7.93 
                 0.05 
                 0.12086 
               
               
                 HS3ST1 
                 205465_x_at 
                 7.91 
                 0.03 
                 0.00249 
               
               
                 CACNA2D1 
                 207050_at 
                 7.9 
                 0.03 
                 0.00314 
               
               
                 FHL1 
                 210299_s_at 
                 7.89 
                 0.1 
                 0.01261 
               
               
                 PHXF1 
                 210191_s_at 
                 7.86 
                 0.04 
                 0.02938 
               
               
                 HXR4 
                 207578_s_at 
                 7.85 
                 0.02 
                 0.00334 
               
               
                 PCDH7 
                 210273_at 
                 7.81 
                 0.06 
                 0.03321 
               
               
                 KCNAB1 
                 208213_s_at 
                 7.81 
                 0.04 
                 0.21222 
               
               
                 PHXF1 
                 205702_at 
                 7.79 
                 0.04 
                 0.07287 
               
               
                 TBL1X 
                 201867_s_at 
                 7.79 
                 0.1 
                 0.17749 
               
               
                 EHD3 
                 218935_at 
                 7.78 
                 0.05 
                 0.03854 
               
               
                 GTF2F2 
                 209595_at 
                 7.78 
                 0.04 
                 0.04245 
               
               
                 LAMC3 
                 219407_s_at 
                 7.78 
                 0.03 
                 0.00270 
               
               
                 EHBP1 
                 212650_at 
                 7.75 
                 0.04 
                 0.11393 
               
               
                 TTF1 
                 204772_s_at 
                 7.75 
                 0.04 
                 0.01049 
               
               
                 GAP43 
                 216963_s_at 
                 7.74 
                 0.03 
                 0.00619 
               
               
                 LEF1 
                 221557_s_at 
                 7.72 
                 0.02 
                 0.00335 
               
               
                 SLC15A2 
                 205316_at 
                 7.69 
                 0.1 
                 0.08613 
               
               
                 RAD52 
                 205647_at 
                 7.68 
                 0.06 
                 0.07622 
               
               
                 BMPR2 
                 209920_at 
                 7.68 
                 0.04 
                 0.05334 
               
               
                 ATAD2B 
                 213387_at 
                 7.66 
                 0.05 
                 0.00089 
               
               
                 BMPR2 
                 210214_s_at 
                 7.66 
                 0.05 
                 0.05113 
               
               
                 COPA 
                 214336_s_at 
                 7.64 
                 0.07 
                 0.02071 
               
               
                 FGGY 
                 219718_at 
                 7.64 
                 0.04 
                 0.06761 
               
               
                 LYST 
                 203518_at 
                 7.63 
                 0.05 
                 0.01240 
               
               
                 DBT 
                 205369_x_at 
                 7.62 
                 0.04 
                 0.01505 
               
               
                 LDB2 
                 206481_s_at 
                 7.62 
                 0.07 
                 0.00034 
               
               
                 NEIL3 
                 219502_at 
                 7.62 
                 0.03 
                 0.24524 
               
               
                 IL15 
                 205992_s_at 
                 7.62 
                 0.1 
                 0.08336 
               
               
                 NRP2 
                 210841_s_at 
                 7.6 
                 0.03 
                 0.00028 
               
               
                 PCDH7 
                 205535_s_at 
                 7.59 
                 0.04 
                 0.10384 
               
               
                 CACNB2 
                 215365_at 
                 7.58 
                 0.04 
                 0.00327 
               
               
                 C1orf21 
                 221272_s_at 
                 7.57 
                 0.04 
                 0.04363 
               
               
                 NRP2 
                 214632_at 
                 7.56 
                 0.03 
                 0.04684 
               
               
                 EPHB2 
                 211165_x_at 
                 7.56 
                 0.04 
                 0.00019 
               
               
                 FHL1 
                 210298_x_at 
                 7.55 
                 0.08 
                 0.05729 
               
               
                 EIF5 
                 208707_at 
                 7.55 
                 0.03 
                 0.06981 
               
               
                 LYST 
                 210943_s_at 
                 7.54 
                 0.04 
                 0.16516 
               
               
                 CASQ2 
                 207317_s_at 
                 7.54 
                 0.04 
                 0.06762 
               
               
                 GOLIM4 
                 204324_s_at 
                 7.53 
                 0.05 
                 0.06101 
               
               
                 ANK2 
                 202920_at 
                 7.53 
                 0.11 
                 0.21165 
               
               
                 ABHD5 
                 218739_at 
                 7.52 
                 0.04 
                 0.00029 
               
               
                 BATF3 
                 220358_at 
                 7.5 
                 0.02 
                 0.09950 
               
               
                 KIT 
                 205051_s_at 
                 7.48 
                 0.06 
                 0.12776 
               
               
                 TGFBRAP1 
                 205210_at 
                 7.47 
                 0.03 
                 0.00931 
               
               
                 PHTF1 
                 215285_s_at 
                 7.45 
                 0.05 
                 0.00664 
               
               
                 FHL1 
                 201539_s_at 
                 7.44 
                 0.07 
                 0.08433 
               
               
                 ESRRG 
                 207981_s_at 
                 7.4 
                 0.09 
                 0.02416 
               
               
                 FHIT 
                 206492_at 
                 7.39 
                 0.05 
                 0.04854 
               
               
                 TRPM8 
                 220226_at 
                 7.39 
                 0.02 
                 0.01284 
               
               
                 NLGN4X 
                 221933_at 
                 7.38 
                 0.12 
                 0.05823 
               
               
                 TSPAN9 
                 205665_at 
                 7.37 
                 0.03 
                 0.06193 
               
               
                 SLC15A2 
                 205317_s_at 
                 7.37 
                 0.05 
                 0.01063 
               
               
                 FAM49A 
                 208092_s_at 
                 7.37 
                 0.04 
                 0.05475 
               
               
                 IL5RA 
                 210744_s_at 
                 7.36 
                 0.02 
                 0.31680 
               
               
                 THRAP3 
                 217847_s_at 
                 7.34 
                 0.03 
                 0.04736 
               
               
                 PDE2A 
                 204134_at 
                 7.34 
                 0.03 
                 0.04255 
               
               
                 MTA1 
                 202247_s_at 
                 7.33 
                 0.03 
                 0.03778 
               
               
                 DBT 
                 205371_s_at 
                 7.32 
                 0.05 
                 0.00536 
               
               
                 PRUNE 
                 209599_s_at 
                 7.32 
                 0.04 
                 0.19033 
               
               
                 PLEKHA2 
                 217677_at 
                 7.3 
                 0.03 
                 0.05817 
               
               
                 WDFY3 
                 212598_at 
                 7.29 
                 0.03 
                 0.05518 
               
               
                 COPA 
                 214337_at 
                 7.29 
                 0.04 
                 0.04946 
               
               
                 PCDH7 
                 205534_at 
                 7.28 
                 0.11 
                 0.12498 
               
               
                 H6PD 
                 206933_s_at 
                 7.28 
                 0.03 
                 0.00634 
               
               
                 CAMTA1 
                 213268_at 
                 7.27 
                 0.07 
                 0.00659 
               
               
                 ARHGAP10 
                 219431_at 
                 7.26 
                 0.04 
                 0.01507 
               
               
                 BTNL8 
                 220421_at 
                 7.26 
                 0.02 
                 0.00210 
               
               
                 TLE4 
                 214688_at 
                 7.25 
                 0.06 
                 0.03273 
               
               
                 SLC4A4 
                 210739_x_at 
                 7.25 
                 0.02 
                 0.03900 
               
               
                 IL15 
                 217371_s_at 
                 7.23 
                 0.06 
                 0.10346 
               
               
                 HHAT 
                 219687_at 
                 7.22 
                 0.04 
                 0.01657 
               
               
                 ABHD5 
                 213805_at 
                 7.22 
                 0.05 
                 0.01621 
               
               
                 TBL1X 
                 201868_s_at 
                 7.22 
                 0.03 
                 0.03174 
               
               
                 PRDM16 
                 220928_s_at 
                 7.21 
                 0.04 
                 0.24362 
               
               
                 NOTCH2 
                 202445_s_at 
                 7.2 
                 0.03 
                 0.19662 
               
               
                 PRDM5 
                 220792_at 
                 7.2 
                 0.02 
                 0.00483 
               
               
                 HTR4 
                 216939_s_at 
                 7.2 
                 0.03 
                 0.00420 
               
               
                 ABHD5 
                 213935_at 
                 7.19 
                 0.04 
                 0.02363 
               
               
                 LYST 
                 215415_s_at 
                 7.19 
                 0.02 
                 0.03630 
               
               
                 DAPK1 
                 211214_s_at 
                 7.19 
                 0.03 
                 0.00220 
               
               
                 TNIK 
                 213107_at 
                 7.18 
                 0.08 
                 0.00314 
               
               
                 FGF12 
                 214589_at 
                 7.17 
                 0.03 
                 0.01345 
               
               
                 GRM8 
                 216256_at 
                 7.17 
                 0.02 
                 0.26278 
               
               
                 MAN1A1 
                 208116_s_at 
                 7.15 
                 0.08 
                 0.10024 
               
               
                 HRG 
                 206226_at 
                 7.15 
                 0.02 
                 0.02982 
               
               
                 TNIK 
                 211828_s_at 
                 7.13 
                 0.08 
                 0.00719 
               
               
                 DYRK1A 
                 211541_s_at 
                 7.13 
                 0.02 
                 0.00907 
               
               
                 CCDC88A 
                 221078_s_at 
                 7.13 
                 0.04 
                 0.00820 
               
               
                 EFHC2 
                 220591_s_at 
                 7.13 
                 0.08 
                 0.00176 
               
               
                 CACNB2 
                 207776_s_at 
                 7.11 
                 0.02 
                 0.07419 
               
               
                 FAM49A 
                 209683_at 
                 7.09 
                 0.05 
                 0.12475 
               
               
                 DEPDC1 
                 220295_x_at 
                 7.08 
                 0.07 
                 0.03224 
               
               
                 ZNF702P 
                 206557_at 
                 7.08 
                 0.05 
                 0.09070 
               
               
                 LPHN3 
                 209867_s_at 
                 7.05 
                 0.05 
                 0.07323 
               
               
                 MFAP3L 
                 210493_s_at 
                 7.05 
                 0.02 
                 0.00583 
               
               
                 ANK2 
                 202921_s_at 
                 7.04 
                 0.03 
                 0.01616 
               
               
                 SLC4A4 
                 203908_at 
                 7.02 
                 0.08 
                 0.04715 
               
               
                 LEF1 
                 210948_s_at 
                 7.02 
                 0.07 
                 0.15749 
               
               
                 HYAL3 
                 211728_s_at 
                 7.02 
                 0.04 
                 0.01476 
               
               
                 PCOLCE2 
                 219295_s_at 
                 7.02 
                 0.06 
                 0.00459 
               
               
                 HS3ST1 
                 205466_s_at 
                 7.02 
                 0.07 
                 0.08931 
               
               
                 MFAP3L 
                 205442_at 
                 7.01 
                 0.07 
                 0.15456 
               
               
                 ESRRG 
                 209966_x_at 
                 7 
                 0.05 
                 0.00785 
               
               
                 KCNAB1 
                 210079_x_at 
                 7 
                 0.02 
                 0.19704 
               
               
                 ABCB4 
                 207819_s_at 
                 7 
                 0.04 
                 0.08178 
               
               
                 DNM3 
                 209839_at 
                 7 
                 0.08 
                 0.00113 
               
               
                 SLC12A6 
                 220740_s_at 
                 6.99 
                 0.02 
                 0.01249 
               
               
                 NRXN1 
                 216096_s_at 
                 6.98 
                 0.02 
                 0.02706 
               
               
                 TNIK 
                 213109_at 
                 6.98 
                 0.05 
                 0.01074 
               
               
                 GLI2 
                 207034_s_at 
                 6.93 
                 0.03 
                 0.00408 
               
               
                 AFF3 
                 205735_s_at 
                 6.93 
                 0.02 
                 0.01012 
               
               
                 KCNAB1 
                 210471_s_at 
                 6.92 
                 0.02 
                 0.16257 
               
               
                 DAB1 
                 220611_at 
                 6.92 
                 0.02 
                 0.03573 
               
               
                 ANK2 
                 216195_at 
                 6.92 
                 0.04 
                 0.09369 
               
               
                 TEC 
                 206301_at 
                 6.91 
                 0.03 
                 0.00424 
               
               
                 WISP1 
                 206796_at 
                 6.9 
                 0.07 
                 0.02554 
               
               
                 NRXN1 
                 209914_s_at 
                 6.9 
                 0.02 
                 0.07166 
               
               
                 MCTP1 
                 220122_at 
                 6.9 
                 0.08 
                 0.00638 
               
               
                 FGF12 
                 207501_s_at 
                 6.9 
                 0.04 
                 0.10060 
               
               
                 IL5RA 
                 207902_at 
                 6.89 
                 0.02 
                 0.00232 
               
               
                 AFF3 
                 205734_s_at 
                 6.89 
                 0.04 
                 0.07308 
               
               
                 RAD52 
                 211904_x_at 
                 6.89 
                 0.02 
                 0.09990 
               
               
                 HTR4 
                 207577_at 
                 6.89 
                 0.03 
                 0.04897 
               
               
                 HS3ST1 
                 213991_s_at 
                 6.88 
                 0.02 
                 0.00154 
               
               
                 FUT9 
                 216185_at 
                 6.88 
                 0.02 
                 0.13109 
               
               
                 DYRK1A 
                 211079_s_at 
                 6.87 
                 0.03 
                 0.09784 
               
               
                 KCNAB1 
                 210078_s_at 
                 6.86 
                 0.05 
                 0.05448 
               
               
                 NRP2 
                 211844_s_at 
                 6.85 
                 0.03 
                 0.07661 
               
               
                 IL5RA 
                 211517_s_at 
                 6.84 
                 0.04 
                 0.11199 
               
               
                 PRKCE 
                 206248_at 
                 6.83 
                 0.02 
                 0.04497 
               
               
                 TBL1X 
                 213401_s_at 
                 6.82 
                 0.02 
                 0.04299 
               
               
                 SPATS2L 
                 215617_at 
                 6.79 
                 0.06 
                 0.00220 
               
               
                 ERBB4 
                 206794_at 
                 6.79 
                 0.05 
                 0.04933 
               
               
                 TRIM48 
                 220534_at 
                 6.78 
                 0.03 
                 0.04251 
               
               
                 ERC2 
                 213938_at 
                 6.78 
                 0.04 
                 0.13941 
               
               
                 ARSE 
                 205894_at 
                 6.75 
                 0.04 
                 0.03859 
               
               
                 WISP1 
                 211312_s_at 
                 6.75 
                 0.02 
                 0.05958 
               
               
                 RAD52 
                 210630_s_at 
                 6.74 
                 0.06 
                 0.12087 
               
               
                 NRXN1 
                 209915_s_at 
                 6.74 
                 0.02 
                 0.00186 
               
               
                 TLE4 
                 216997_x_at 
                 6.72 
                 0.03 
                 0.00394 
               
               
                 CACNB2 
                 213714_at 
                 6.7 
                 0.03 
                 0.09479 
               
               
                 SLC4A4 
                 211494_s_at 
                 6.69 
                 0.02 
                 0.04014 
               
               
                 EPB41 
                 214530_x_at 
                 6.67 
                 0.02 
                 0.11757 
               
               
                 PTGS2 
                 204748_at 
                 6.66 
                 0.1 
                 0.07900 
               
               
                 LRCH1 
                 214936_at 
                 6.65 
                 0.02 
                 0.19740 
               
               
                 LPHN3 
                 209866_s_at 
                 6.62 
                 0.09 
                 0.02648 
               
               
                 SP4 
                 206663_at 
                 6.6 
                 0.02 
                 0.03413 
               
               
                 MFAP3L 
                 210843_s_at 
                 6.58 
                 0.03 
                 0.05724 
               
               
                 NTNG1 
                 206713_at 
                 6.56 
                 0.02 
                 0.15772 
               
               
                 GRM8 
                 216992_s_at 
                 6.56 
                 0.03 
                 0.00917 
               
               
                 SNTG2 
                 220487_at 
                 6.48 
                 0.02 
                 0.09169 
               
               
                 CCDC88A 
                 219387_at 
                 6.48 
                 0.03 
                 0.00943 
               
               
                 MFAP3L 
                 210492_at 
                 6.46 
                 0.02 
                 0.27020 
               
               
                 EPB41 
                 207793_s_at 
                 6.43 
                 0.02 
                 0.14880 
               
               
                 CUL3 
                 201372_s_at 
                 6.38 
                 0.02 
                 0.04445 
               
               
                 PTPRZ1 
                 204469_at 
                 6.37 
                 0.03 
                 0.02128 
               
               
                 NRP2 
                 210842_at 
                 6.37 
                 0.02 
                 0.01312 
               
               
                 PDZK1 
                 205380_at 
                 6.32 
                 0.09 
                 0.00382 
               
               
                 DPPA4 
                 219651_at 
                 6.32 
                 0.07 
                 0.06463 
               
               
                 SLC4A4 
                 210738_s_at 
                 6.27 
                 0.03 
                 0.00763 
               
               
                 GRM8 
                 216255_s_at 
                 6.26 
                 0.03 
                 0.11487 
               
               
                 GAP43 
                 204471_at 
                 6.19 
                 0.03 
                 0.01214 
               
               
                 DBT 
                 211196_at 
                 6.18 
                 0.02 
                 0.02234 
               
               
                 CASC5 
                 220247_at 
                 6.17 
                 0.01 
                 0.07876 
               
               
                 LRP1B 
                 219643_at 
                 6.14 
                 0.03 
                 0.00130 
               
               
                 IL5RA 
                 211516_at 
                 6.14 
                 0.01 
                 0.04613 
               
               
                 PCDH7 
                 210941_at 
                 6.13 
                 0.04 
                 0.18964 
               
               
                 EFHC2 
                 220523_at 
                 6.12 
                 0.02 
                 0.00047 
               
               
                 FUT9 
                 214046_at 
                 6.08 
                 0.07 
                 0.13738 
               
               
                 FUT9 
                 207696_at 
                 5.96 
                 0.01 
                 0.23998 
               
               
                 PDE6C 
                 211093_at 
                 5.91 
                 0.01 
                 0.00334 
               
               
                   
               
               
                 Median expr = median log expression value across the samples; CV = coefficient of variation of the log expression values; Surv. P value = survival p-value. 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 4 
               
             
            
               
                   
               
               
                 Genes CN-invariant in the TCGA EOC samples and insignificant 
               
               
                 for survival in both GSE9899 and TCGA patient cohorts. 
               
            
           
           
               
               
               
               
               
               
            
               
                 Symbol 
                 Refseq 
                 Chr 
                 Start 
                 End 
                 Description 
               
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 AFF3 
                 NM_001025108 
                 chr2 
                 100163715 
                 100722045 
                 AF4/FMR2 family 
               
               
                   
                   
                   
                   
                   
                 member 3 isoform 
               
               
                   
                   
                   
                   
                   
                 2 
               
               
                 AMD1 
                 NM_001287216 
                 chr6 
                 111195986 
                 111216915 
                 S- 
               
               
                   
                   
                   
                   
                   
                 adenosylmethionine 
               
               
                   
                   
                   
                   
                   
                 decarboxylase 
               
               
                   
                   
                   
                   
                   
                 proenzyme isoform 
               
               
                   
                   
                   
                   
                   
                 5 
               
               
                 ANK2 
                 NM_001127493 
                 chr4 
                 113739238 
                 114304896 
                 ankyrin-2 isoform 3 
               
               
                 ARHGAP10 
                 NM_024605 
                 chr4 
                 148653452 
                 148993927 
                 rho GTPase- 
               
               
                   
                   
                   
                   
                   
                 activating protein 
               
               
                   
                   
                   
                   
                   
                 10 
               
               
                 ATF7IP2 
                 NM_024997 
                 chr16 
                 10479911 
                 10577495 
                 activating 
               
               
                   
                   
                   
                   
                   
                 transcription factor 
               
               
                   
                   
                   
                   
                   
                 7-interacting 
               
               
                   
                   
                   
                   
                   
                 protein 2 isoform 1 
               
               
                 BATF3 
                 NM_018664 
                 chr1 
                 212859758 
                 212873327 
                 basic leucine zipper 
               
               
                   
                   
                   
                   
                   
                 transcriptional 
               
               
                   
                   
                   
                   
                   
                 factor ATF-like 3 
               
               
                 BRE 
                 NM_199194 
                 chr2 
                 28113481 
                 28561767 
                 BRCA1-A complex 
               
               
                   
                   
                   
                   
                   
                 subunit BRE 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 CASC5 
                 NM_170589 
                 chr15 
                 40886446 
                 40954881 
                 protein CASC5 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 CCDC88A 
                 NM_018084 
                 chr2 
                 55514977 
                 55647057 
                 girdin isoform 2 
               
               
                 CLMN 
                 NM_024734 
                 chr14 
                 95648275 
                 95786245 
                 calmin 
               
               
                 CUL3 
                 NM_001257197 
                 chr2 
                 225334866 
                 225450114 
                 cullin-3 isoform 2 
               
               
                 DAPK1 
                 NM_001288729 
                 chr9 
                 90113449 
                 90323549 
                 death-associated 
               
               
                   
                   
                   
                   
                   
                 protein kinase 1 
               
               
                 DEPDC1 
                 NM_001114120 
                 chr1 
                 68939834 
                 68962904 
                 DEP domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 
               
               
                   
                   
                   
                   
                   
                 1A isoform a 
               
               
                 EPHB2 
                 NM_004442 
                 chr1 
                 23037330 
                 23241823 
                 ephrin type-B 
               
               
                   
                   
                   
                   
                   
                 receptor 2 isoform 
               
               
                   
                   
                   
                   
                   
                 2 precursor 
               
               
                 ESRRG 
                 NM_206594 
                 chr1 
                 216676587 
                 217262987 
                 estrogen-related 
               
               
                   
                   
                   
                   
                   
                 receptor gamma 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 FGF12 
                 NM_004113 
                 chr3 
                 191857181 
                 192445388 
                 fibroblast growth 
               
               
                   
                   
                   
                   
                   
                 factor 12 isoform 2 
               
               
                 FHL1 
                 NM_001159702 
                 chrX 
                 135229558 
                 135293518 
                 four and a half LIM 
               
               
                   
                   
                   
                   
                   
                 domains protein 1 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 FUT9 
                 NM_006581 
                 chr6 
                 96463844 
                 96663488 
                 alpha-(1,3)- 
               
               
                   
                   
                   
                   
                   
                 fucosyltransferase 9 
               
               
                 GBE1 
                 NM_000158 
                 chr3 
                 81538849 
                 81810950 
                 1,4-alpha-glucan- 
               
               
                   
                   
                   
                   
                   
                 branching enzyme 
               
               
                 HTR4 
                 NM_199453 
                 chr5 
                 147830594 
                 148016624 
                 5- 
               
               
                   
                   
                   
                   
                   
                 hydroxytryptamine 
               
               
                   
                   
                   
                   
                   
                 receptor 4 isoform 
               
               
                   
                   
                   
                   
                   
                 g 
               
               
                 HYAL3 
                 NM_003549 
                 chr3 
                 50330258 
                 50336899 
                 hyaluronidase-3 
               
               
                   
                   
                   
                   
                   
                 isoform 1 precursor 
               
               
                 IL5RA 
                 NM_175726 
                 chr3 
                 3108007 
                 3152058 
                 interleukin-5 
               
               
                   
                   
                   
                   
                   
                 receptor subunit 
               
               
                   
                   
                   
                   
                   
                 alpha isoform 1 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 KCNAB1 
                 NM_172159 
                 chr3 
                 156008775 
                 156256927 
                 voltage-gated 
               
               
                   
                   
                   
                   
                   
                 potassium channel 
               
               
                   
                   
                   
                   
                   
                 subunit beta-1 
               
               
                   
                   
                   
                   
                   
                 isoform 3 
               
               
                 LDB2 
                 NM_001290 
                 chr4 
                 16503164 
                 16900424 
                 LIM domain- 
               
               
                   
                   
                   
                   
                   
                 binding protein 2 
               
               
                   
                   
                   
                   
                   
                 isoform a 
               
               
                 LEF1 
                 NM_001130714 
                 chr4 
                 108968700 
                 109090112 
                 lymphoid enhancer- 
               
               
                   
                   
                   
                   
                   
                 binding factor 1 
               
               
                   
                   
                   
                   
                   
                 isoform 3 
               
               
                 LRCH1 
                 NM_015116 
                 chr13 
                 47127295 
                 47319036 
                 leucine-rich repeat 
               
               
                   
                   
                   
                   
                   
                 and calponin 
               
               
                   
                   
                   
                   
                   
                 homology domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 1 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 MFAP3L 
                 NM_021647 
                 chr4 
                 170907747 
                 170947581 
                 microfibrillar- 
               
               
                   
                   
                   
                   
                   
                 associated protein 
               
               
                   
                   
                   
                   
                   
                 3-like isoform 1 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 MTR 
                 NM_001291939 
                 chr1 
                 236958580 
                 237067281 
                 methionine 
               
               
                   
                   
                   
                   
                   
                 synthase isoform 2 
               
               
                 NMD3 
                 NM_015938 
                 chr3 
                 160939098 
                 160969795 
                 60S ribosomal 
               
               
                   
                   
                   
                   
                   
                 export protein 
               
               
                   
                   
                   
                   
                   
                 NMD3 
               
               
                 NOTCH2 
                 NM_024408 
                 chr1 
                 120454175 
                 120612317 
                 neurogenic locus 
               
               
                   
                   
                   
                   
                   
                 notch homolog 
               
               
                   
                   
                   
                   
                   
                 protein 2 isoform 1 
               
               
                   
                   
                   
                   
                   
                 preproprotein 
               
               
                 NRP2 
                 NM_018534 
                 chr2 
                 206547223 
                 206641880 
                 neuropilin-2 
               
               
                   
                   
                   
                   
                   
                 isoform 4 precursor 
               
               
                 NTNG1 
                 NM_014917 
                 chr1 
                 107682744 
                 108024475 
                 netrin-G1 isoform 3 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 PARN 
                 NM_001134477 
                 chr16 
                 14529556 
                 14724128 
                 poly(A)-specific 
               
               
                   
                   
                   
                   
                   
                 ribonuclease PARN 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 PRKCZ 
                 NM_001033582 
                 chr1 
                 2036154 
                 2116834 
                 protein kinase C 
               
               
                   
                   
                   
                   
                   
                 zeta type isoform 2 
               
               
                 PRUNE 
                 NM_021222 
                 chr1 
                 150980972 
                 151008189 
                 protein prune 
               
               
                   
                   
                   
                   
                   
                 homolog isoform 1 
               
               
                 PUM1 
                 NM_014676 
                 chr1 
                 31404352 
                 31538564 
                 pumilio homolog 1 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 RNF144A 
                 NM_014746 
                 chr2 
                 7057522 
                 7184309 
                 E3 ubiquitin- 
               
               
                   
                   
                   
                   
                   
                 protein ligase 
               
               
                   
                   
                   
                   
                   
                 RNF144A 
               
               
                 SCHIP1 
                 NM_014575 
                 chr3 
                 158991035 
                 159615155 
                 schwannomin- 
               
               
                   
                   
                   
                   
                   
                 interacting protein 
               
               
                   
                   
                   
                   
                   
                 1 isoform 1 
               
               
                 SLC12A6 
                 NM_001042495 
                 chr15 
                 34522196 
                 34630265 
                 solute carrier 
               
               
                   
                   
                   
                   
                   
                 family 12 member 
               
               
                   
                   
                   
                   
                   
                 6 isoform c 
               
               
                 SLC4A4 
                 NM_003759 
                 chr4 
                 72204769 
                 72437804 
                 electrogenic 
               
               
                   
                   
                   
                   
                   
                 sodium bicarbonate 
               
               
                   
                   
                   
                   
                   
                 cotransporter 1 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 SP4 
                 NM_003112 
                 chr7 
                 21467688 
                 21554151 
                 transcription factor 
               
               
                   
                   
                   
                   
                   
                 Sp4 
               
               
                 TBL1X 
                 NM_001139468 
                 chrX 
                 9431334 
                 9687780 
                 F-box-like/WD 
               
               
                   
                   
                   
                   
                   
                 repeat-containing 
               
               
                   
                   
                   
                   
                   
                 protein TBL1X 
               
               
                   
                   
                   
                   
                   
                 isoform b 
               
               
                 TLE4 
                 NM_007005 
                 chr9 
                 82186687 
                 82341796 
                 transducin-like 
               
               
                   
                   
                   
                   
                   
                 enhancer protein 4 
               
               
                   
                   
                   
                   
                   
                 isoform 3 
               
               
                 TNIK 
                 NM_001161561 
                 chr3 
                 170780291 
                 171178197 
                 TRAF2 and NCK- 
               
               
                   
                   
                   
                   
                   
                 interacting protein 
               
               
                   
                   
                   
                   
                   
                 kinase isoform 3 
               
               
                 TSPAN9 
                 NM_001168320 
                 chr12 
                 3186520 
                 3395730 
                 tetraspanin-9 
               
               
                 WDFY3 
                 NM_014991 
                 chr4 
                 85590692 
                 85887544 
                 WD repeat and 
               
               
                   
                   
                   
                   
                   
                 FYVE domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 3 
               
               
                 ZNF274 
                 NM_133502 
                 chr19 
                 58694355 
                 58724928 
                 neurotrophin 
               
               
                   
                   
                   
                   
                   
                 receptor-interacting 
               
               
                   
                   
                   
                   
                   
                 factor homolog 
               
               
                   
                   
                   
                   
                   
                 isoform c 
               
               
                 ZNF702P 
                 NR_003578 
                 chr19 
                 53471503 
                 53496784 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 5 
               
             
            
               
                   
               
               
                 Genes that are CN-invariant in normal human tissues, 
               
               
                 located in CN-invariant cytobands of EOC tumors. 
               
            
           
           
               
               
               
               
               
               
            
               
                 Symbol 
                 Refseq 
                 Chr 
                 Start 
                 End 
                 Description 
               
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 AZIN2 
                 NM_052998 
                 chr1 
                 33546713 
                 33586132 
                 antizyme inhibitor 
               
               
                   
                   
                   
                   
                   
                 2 isoform 1 
               
               
                 BATF3 
                 NM_018664 
                 chr1 
                 212859758 
                 212873327 
                 basic leucine zipper 
               
               
                   
                   
                   
                   
                   
                 transcriptional 
               
               
                   
                   
                   
                   
                   
                 factor ATF-like 3 
               
               
                 DEPDC1 
                 NM_001114120 
                 chr1 
                 68939834 
                 68962904 
                 DEP domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 
               
               
                   
                   
                   
                   
                   
                 1A isoform a 
               
               
                 EHD3 
                 NM_014600 
                 chr2 
                 31456879 
                 31491260 
                 EH domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 
               
               
                   
                   
                   
                   
                   
                 3 
               
               
                 FAHD2A 
                 NM_016044 
                 chr2 
                 96068447 
                 96078879 
                 fumarylacetoacetate 
               
               
                   
                   
                   
                   
                   
                 hydrolase domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 
               
               
                   
                   
                   
                   
                   
                 2A 
               
               
                 FAM132B 
                 NM_001291832 
                 chr2 
                 239067648 
                 239077532 
                 erythroferrone 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 FHL2 
                 NM_201557 
                 chr2 
                 105977282 
                 106055230 
                 four and a half LIM 
               
               
                   
                   
                   
                   
                   
                 domains protein 2 
               
               
                 HS3ST1 
                 NM_005114 
                 chr4 
                 11399987 
                 11430537 
                 heparan sulfate 
               
               
                   
                   
                   
                   
                   
                 glucosamine 3-O- 
               
               
                   
                   
                   
                   
                   
                 sulfotransferase 1 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 IDO2 
                 NM_194294 
                 chr8 
                 39792473 
                 39873910 
                 indoleamine 2,3- 
               
               
                   
                   
                   
                   
                   
                 dioxygenase 2 
               
               
                 LIN54 
                 NM_001115008 
                 chr4 
                 83845756 
                 83931987 
                 protein lin-54 
               
               
                   
                   
                   
                   
                   
                 homolog isoform b 
               
               
                 LINC00578 
                 NR_047568 
                 chr3 
                 177159708 
                 177470492 
               
               
                 LINC00882 
                 NR_028303 
                 chr3 
                 106828636 
                 106959485 
               
               
                 LINC01001 
                 NR_028326 
                 chr11 
                 126986 
                 131920 
               
               
                 LINC01091 
                 NR_027106 
                 chr4 
                 124695418 
                 124786730 
               
               
                 LMCD1-AS1 
                 NR_033378 
                 chr3 
                 8262833 
                 8543344 
               
               
                 LOC100506457 
                 NR_110198 
                 chr2 
                 12147241 
                 12223743 
               
               
                 LOC101926942 
                 NR_110657 
                 chr10 
                 92162277 
                 92300562 
               
               
                 LOC101927905 
                 NR_120455 
                 chr12 
                 8388010 
                 8391553 
               
               
                 LOC391003 
                 NM_001099850 
                 chr1 
                 13035498 
                 13039011 
                 PRAME family 
               
               
                   
                   
                   
                   
                   
                 member-like 
               
               
                 LOC440700 
                 NR_036683 
                 chr1 
                 165667986 
                 165679199 
               
               
                 LOC729970 
                 NR_033998 
                 chr1 
                 95393583 
                 95428826 
               
               
                 MALRD1 
                 NM_001142308 
                 chr10 
                 19337699 
                 20023407 
                 MAM and LDL- 
               
               
                   
                   
                   
                   
                   
                 receptor class A 
               
               
                   
                   
                   
                   
                   
                 domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 1 precursor 
               
               
                 MIR5694 
                 NR_049879 
                 chr10 
                 122344590 
                 122806858 
               
               
                 MRPL47 
                 NM_020409 
                 chr3 
                 179306254 
                 179322434 
                 39S ribosomal 
               
               
                   
                   
                   
                   
                   
                 protein L47, 
               
               
                   
                   
                   
                   
                   
                 mitochondrial 
               
               
                   
                   
                   
                   
                   
                 isoform a 
               
               
                 NAA16 
                 NM_024561 
                 chr13 
                 41885340 
                 41951166 
                 N-alpha- 
               
               
                   
                   
                   
                   
                   
                 acetyltransferase 
               
               
                   
                   
                   
                   
                   
                 16, NatA auxiliary 
               
               
                   
                   
                   
                   
                   
                 subunit isoform 1 
               
               
                 NBPF8 
                 NR_102404 
                 chr1 
                 147574322 
                 148346929 
               
               
                 NMD3 
                 NM_015938 
                 chr3 
                 160939098 
                 160969795 
                 60S ribosomal 
               
               
                   
                   
                   
                   
                   
                 export protein 
               
               
                   
                   
                   
                   
                   
                 NMD3 
               
               
                 NUP133 
                 NM_018230 
                 chr1 
                 229577043 
                 229644088 
                 nuclear pore 
               
               
                   
                   
                   
                   
                   
                 complex protein 
               
               
                   
                   
                   
                   
                   
                 Nup133 
               
               
                 NYAP2 
                 NM_020864 
                 chr2 
                 226265601 
                 226518734 
                 neuronal tyrosine- 
               
               
                   
                   
                   
                   
                   
                 phosphorylated 
               
               
                   
                   
                   
                   
                   
                 phosphoinositide-3- 
               
               
                   
                   
                   
                   
                   
                 kinase adapter 2 
               
               
                 PTCHD1-AS 
                 NR_073010 
                 chrX 
                 22277913 
                 23311263 
               
               
                 RAI2 
                 NM_001172743 
                 chrX 
                 17818168 
                 17879457 
                 retinoic acid- 
               
               
                   
                   
                   
                   
                   
                 induced protein 2 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 RGS18 
                 NM_130782 
                 chr1 
                 192127591 
                 192154945 
                 regulator of G- 
               
               
                   
                   
                   
                   
                   
                 protein signaling 18 
               
               
                 SEPSECS-AS1 
                 NR_037934 
                 chr4 
                 25162293 
                 25200127 
               
               
                 SRGAP2C 
                 NM_001271872 
                 chr1 
                 206516199 
                 206581301 
                 SLIT-ROBO Rho 
               
               
                   
                   
                   
                   
                   
                 GTPase-activating 
               
               
                   
                   
                   
                   
                   
                 protein 2C 
               
               
                 TC2N 
                 NM_152332 
                 chr14 
                 92246095 
                 92302870 
                 tandem C2 domains 
               
               
                   
                   
                   
                   
                   
                 nuclear protein 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 TCEANC2 
                 NM_153035 
                 chr1 
                 54519273 
                 54565416 
                 transcription 
               
               
                   
                   
                   
                   
                   
                 elongation factor A 
               
               
                   
                   
                   
                   
                   
                 N-terminal and 
               
               
                   
                   
                   
                   
                   
                 central domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 
               
               
                   
                   
                   
                   
                   
                 2 
               
               
                 TENM3 
                 NM_001080477 
                 chr4 
                 183245136 
                 183724177 
                 teneurin-3 
               
               
                 TEX41 
                 NR_033870 
                 chr2 
                 145425533 
                 145834291 
               
               
                 TGFBRAP1 
                 NM_004257 
                 chr2 
                 105880846 
                 105946171 
                 transforming 
               
               
                   
                   
                   
                   
                   
                 growth factor-beta 
               
               
                   
                   
                   
                   
                   
                 receptor-associated 
               
               
                   
                   
                   
                   
                   
                 protein 1 
               
               
                 WISP1 
                 NM_080838 
                 chr8 
                 134203281 
                 134243932 
                 WNT1-inducible- 
               
               
                   
                   
                   
                   
                   
                 signaling pathway 
               
               
                   
                   
                   
                   
                   
                 protein 1 isoform 2 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 YEATS2 
                 NM_018023 
                 chr3 
                 183415605 
                 183530413 
                 YEATS domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 
               
               
                   
                   
                   
                   
                   
                 2 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 6 
               
             
            
               
                   
               
               
                 Primers. 
               
            
           
           
               
               
               
               
               
            
               
                 Target gene 
                 Forward 
                 SEQ ID NO 
                 Reverse 
                 SEQ ID NO 
               
               
                   
               
            
           
           
               
            
               
                 Primer set 1 
               
            
           
           
               
               
               
               
               
            
               
                 XRCC5 
                 AGGTCGTGGATGTATGGGGA 
                 1 
                 GGCCGCATCCAACTTGTTTT 
                 2 
               
               
                 AUTS2 
                 GTAAGGTGCACGTTTCCTGA 
                 3 
                 CTCTAACTCGCGATGGCTCC 
                 4 
               
               
                 EIF5 
                 ACCGAGAACTCTTGCAGTCG 
                 5 
                 AGAACTGGTCTGACACGCTG 
                 6 
               
               
                 PARN 
                 CCCACCATAGCTGCCTGAAA 
                 7 
                 CATACGGCAAGCCCTCTCAT 
                 8 
               
               
                 YEATS2 
                 CCCGAGTGCCCATCATCATT 
                 9 
                 CCTTCTGTACTTGCAGCCCT 
                 10 
               
               
                 FHL2 
                 GAAGTGCTCCCTCTCACTGG 
                 11 
                 GCAAGATTGCCTGGGTGAGA 
                 12 
               
               
                   
               
            
           
           
               
            
               
                 Primer set 2 
               
            
           
           
               
               
               
               
               
            
               
                 XRCC5 
                 ACCAAGTGGAGACACAGCAG 
                 13 
                 TCCCCATACATCCACGACCT 
                 14 
               
               
                 AUTS2 
                 TGTAAGGTGCACGTTTCCTG 
                 15 
                 AGGTTGACCTGTTACGGCTG 
                 16 
               
               
                 EIF5 
                 CTGTCAATGTCAACCGCAGC 
                 17 
                 GCCTTTGCAACGTCAACCAT 
                 18 
               
               
                 PARN 
                 GTGGCGCTGTGTTCACTTTC 
                 19 
                 AATGGGCTGGGACATGTTGT 
                 20 
               
               
                 YEATS2 
                 AGGAATGACGGGGACTCCAT 
                 21 
                 AATGATGATGGGCACTCGGG 
                 22 
               
               
                 FHL2 
                 TCGAGTAAGGCACACCCAAA 
                 23 
                 TAGACTTGACGCAACGGGAG 
                 24 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 7 
               
             
            
               
                   
               
               
                 Worldwide ten most frequent cancers used in the present 
               
               
                 examples. The samples data has been obtained from TCGA 
               
            
           
           
               
               
               
            
               
                 Name 
                 Frequency, % 
                 Sample size 
               
               
                   
               
            
           
           
               
               
               
            
               
                 Breast invasive carcinoma 
                 12 
                 1096 
               
               
                 Ovarian serous adenocarcinoma 
                 1.7 
                 593 
               
               
                 Head and neck squamous cell 
                 5 
                 524 
               
               
                 carcinoma 
               
               
                 Lung adenocarcinoma 
                 2.5 
                 518 
               
               
                 Lung squamous cell carcinoma 
                 6.6 
                 501 
               
               
                 Prostate adenocarcinoma 
                 7.9 
                 493 
               
               
                 Colon adenocarcinoma 
                 9.5 
                 454 
               
               
                 Stomach adenocarcinoma 
                 6.1 
                 442 
               
               
                 Liver hepatocellular carcinoma 
                 4.5 
                 372 
               
               
                 Cervical squamous cell carcinoma 
                 3.1 
                 297 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 8 
               
             
            
               
                   
               
               
                 The candidate reference loci for use with the 10 most frequent cancers listed in Table 7. 
               
            
           
           
               
               
               
               
               
               
            
               
                 Symbol 
                 Refseq 
                 Chr 
                 Start 
                 End 
                 Description 
               
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 ALG10 
                 NM_032834 
                 chr12 
                 34175215 
                 34181236 
                 dol-P- 
               
               
                   
                   
                   
                   
                   
                 Glc:Glc(2)Man(9)GlcNAc(2)- 
               
               
                   
                   
                   
                   
                   
                 PP-Dol alpha-1,2- 
               
               
                   
                   
                   
                   
                   
                 glucosyltransferase 
               
               
                 ANKRD20A9P 
                 NR_027995 
                 chr13 
                 19408542 
                 19446109 
               
               
                 AUTS2 
                 NM_015570 
                 chr7 
                 69063904 
                 70258054 
                 autism susceptibility gene 2 
               
               
                   
                   
                   
                   
                   
                 protein isoform 1 
               
               
                 BAGE 
                 NM_001187 
                 chr21 
                 11057795 
                 11098937 
                 B melanoma antigen 1 precursor 
               
               
                 BAGE2 
                 NM_182482 
                 chr21 
                 11020841 
                 11098925 
                 B melanoma antigen 2 precursor 
               
               
                 BAGE3 
                 NM_182481 
                 chr21 
                 11020841 
                 11098925 
                 B melanoma antigen 3 precursor 
               
               
                 BAGE4 
                 NM_181704 
                 chr21 
                 11020841 
                 11098925 
                 B melanoma antigen 4 precursor 
               
               
                 BAGE5 
                 NM_182484 
                 chr21 
                 11020841 
                 11098925 
                 B melanoma antigen 5 precursor 
               
               
                 CALN1 
                 NM_001017440 
                 chr7 
                 71244475 
                 71802208 
                 calcium-binding protein 8 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 CDH12 
                 NM_004061 
                 chr5 
                 21750972 
                 22853731 
                 cadherin-12 preproprotein 
               
               
                 CDH18 
                 NM_004934 
                 chr5 
                 19473154 
                 19988353 
                 cadherin-18 isoform 1 
               
               
                   
                   
                   
                   
                   
                 preproprotein 
               
               
                 CHEK2P2 
                 NR_038836 
                 chr15 
                 20487996 
                 20496811 
               
               
                 CNTNAP3B 
                 NM_001201380 
                 chr9 
                 43684884 
                 43922473 
                 contactin-associated protein-like 
               
               
                   
                   
                   
                   
                   
                 3B precursor 
               
               
                 CNTNAP3P2 
                 NR_111893 
                 chr9 
                 43685195 
                 43921493 
               
               
                 CSMD1 
                 NM_033225 
                 chr8 
                 2792874 
                 4852328 
                 CUB and sushi domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 1 precursor 
               
               
                 DDX3Y 
                 NM_001122665 
                 chrY 
                 15016018 
                 15030439 
                 ATP-dependent RNA helicase 
               
               
                   
                   
                   
                   
                   
                 DDX3Y isoform 1 
               
               
                 FAM133A 
                 NM_173698 
                 chrX 
                 92929011 
                 92967273 
                 protein FAM133A 
               
               
                 FAM135B 
                 NM_015912 
                 chr8 
                 139142265 
                 139509065 
                 protein FAM135B 
               
               
                 FAM27C 
                 NR_027421 
                 chr9 
                 44990235 
                 44991492 
               
               
                 FAM27E2 
                 NR_103714 
                 chr9 
                 46385603 
                 46387373 
               
               
                 FAM74A1 
                 NR_026803 
                 chr9 
                 65488295 
                 65494240 
               
               
                 FAM74A4 
                 NR_110998 
                 chr9 
                 65487272 
                 65494386 
               
               
                 FAM74A6 
                 NR_110999 
                 chr9 
                 65488295 
                 65494240 
               
               
                 GBE1 
                 NM_000158 
                 chr3 
                 81538849 
                 81810950 
                 1,4-alpha-glucan-branching 
               
               
                   
                   
                   
                   
                   
                 enzyme 
               
               
                 GUSBP1 
                 NR_027028 
                 chr5 
                 21459588 
                 21497305 
               
               
                 GYG2P1 
                 NR_033667 
                 chrY 
                 14517914 
                 14533389 
               
               
                 HERC2P3 
                 NR_036432 
                 chr15 
                 20613649 
                 20711433 
               
               
                 KGFLP1 
                 NR_003674 
                 chr9 
                 46687556 
                 46746820 
               
               
                 KHDRBS3 
                 NM_006558 
                 chr8 
                 136469715 
                 136659848 
                 KH domain-containing, RNA- 
               
               
                   
                   
                   
                   
                   
                 binding, signal transduction- 
               
               
                   
                   
                   
                   
                   
                 associated protein 3 
               
               
                 LINC00417 
                 NR_047508 
                 chr13 
                 19312239 
                 19314239 
               
               
                 LINC01189 
                 NR_046203 
                 chr9 
                 46763790 
                 46833319 
               
               
                 LOC100507468 
                 NR_108105 
                 chr7 
                 69061123 
                 69062481 
               
               
                 LOC101927827 
                 NR_121564 
                 chr9 
                 44384584 
                 44391314 
               
               
                 LOC101928201 
                 NR_110390 
                 chrX 
                 4545240 
                 4551613 
               
               
                 LOC102723427 
                 NR_120514 
                 chr7 
                 67485239 
                 67497677 
               
               
                 MIR3648-1 
                 NR_037421 
                 chr21 
                 9825831 
                 9826011 
               
               
                 MIR3687-1 
                 NR_037458 
                 chr21 
                 9826202 
                 9826263 
               
               
                 MIR3914-1 
                 NR_037477 
                 chr7 
                 70772657 
                 70772756 
               
               
                 MIR3914-2 
                 NR_037479 
                 chr7 
                 70772659 
                 70772754 
               
               
                 MIR4275 
                 NR_036237 
                 chr4 
                 28821203 
                 28821290 
               
               
                 MIR4650-1 
                 NR_039793 
                 chr7 
                 72162873 
                 72162949 
               
               
                 MIR4650-2 
                 NR_039794 
                 chr7 
                 72162873 
                 72162949 
               
               
                 NAP1L3 
                 NM_004538 
                 chrX 
                 92925924 
                 92928682 
                 nucleosome assembly protein 1- 
               
               
                   
                   
                   
                   
                   
                 like 3 
               
               
                 NLGN4X 
                 NM_181332 
                 chrX 
                 5808066 
                 6146923 
                 neuroligin-4, X-linked 
               
               
                 PCDH11X 
                 NM_032968 
                 chrX 
                 91090459 
                 91878228 
                 protocadherin-11 X-linked 
               
               
                   
                   
                   
                   
                   
                 isoform c precursor 
               
               
                 PCDH7 
                 NM_032456 
                 chr4 
                 30722029 
                 30726957 
                 protocadherin-7 isoform b 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 PCDH9 
                 NM_203487 
                 chr13 
                 66876965 
                 67804468 
                 protocadherin-9 isoform 1 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 PCDH9-AS2 
                 NR_046527 
                 chr13 
                 67399300 
                 67489163 
               
               
                 PCDH9-AS3 
                 NR_046636 
                 chr13 
                 67551520 
                 67559908 
               
               
                 PCDH9-AS4 
                 NR_046637 
                 chr13 
                 67565017 
                 67576132 
               
               
                 PFKP 
                 NM_001242339 
                 chr10 
                 3110818 
                 3178997 
                 ATP-dependent 6- 
               
               
                   
                   
                   
                   
                   
                 phosphofructokinase, platelet 
               
               
                   
                   
                   
                   
                   
                 type isoform 2 
               
               
                 PITRM1 
                 NM_014889 
                 chr10 
                 3179918 
                 3215033 
                 presequence protease, 
               
               
                   
                   
                   
                   
                   
                 mitochondrial isoform 2 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 PITRM1-AS1 
                 NR_038284 
                 chr10 
                 3183792 
                 3190821 
               
               
                 PMCHL1 
                 NR_003921 
                 chr5 
                 22142460 
                 22152379 
               
               
                 PXDNL 
                 NM_144651 
                 chr8 
                 52232136 
                 52722005 
                 peroxidasin-like protein 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 ROBO1 
                 NM_133631 
                 chr3 
                 78646387 
                 79068609 
                 roundabout homolog 1 isoform 
               
               
                   
                   
                   
                   
                   
                 b 
               
               
                 SPATA31A5 
                 NM_001113541 
                 chr9 
                 65503362 
                 65509610 
                 spermatogenesis-associated 
               
               
                   
                   
                   
                   
                   
                 protein 31A5 
               
               
                 SPATA31A6 
                 NM_001145196 
                 chr9 
                 43624501 
                 43630730 
                 spermatogenesis-associated 
               
               
                   
                   
                   
                   
                   
                 protein 31A6 
               
               
                 SPATA31A7 
                 NM_015667 
                 chr9 
                 65503365 
                 65509610 
                 spermatogenesis-associated 
               
               
                   
                   
                   
                   
                   
                 protein 31A7 
               
               
                 SYT10 
                 NM_198992 
                 chr12 
                 33528347 
                 33592754 
                 synaptotagmin-10 
               
               
                 TEKT4P2 
                 NR_038329 
                 chr21 
                 9915249 
                 9968594 
               
               
                 TPTE 
                 NM_199259 
                 chr21 
                 10906186 
                 10990943 
                 putative tyrosine-protein 
               
               
                   
                   
                   
                   
                   
                 phosphatase TPTE isoform beta 
               
               
                 TTTY15 
                 NR_001545 
                 chrY 
                 14774297 
                 14804153 
               
               
                 TYW1B 
                 NM_001145440 
                 chr7 
                 72039491 
                 72298813 
                 S-adenosyl-L-methionine- 
               
               
                   
                   
                   
                   
                   
                 dependent tRNA 4- 
               
               
                   
                   
                   
                   
                   
                 demethylwyosine synthase 
               
               
                 USP9Y 
                 NM_004654 
                 chrY 
                 14813159 
                 14972768 
                 probable ubiquitin carboxyl- 
               
               
                   
                   
                   
                   
                   
                 terminal hydrolase FAF-Y 
               
               
                 WBSCR17 
                 NM_022479 
                 chr7 
                 70597522 
                 71178586 
                 putative polypeptide N- 
               
               
                   
                   
                   
                   
                   
                 acetylgalactosaminyltransferase- 
               
               
                   
                   
                   
                   
                   
                 like protein 3 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 9 
               
             
            
               
                   
               
               
                 The candidate reference loci for use with cancer-unaffected 
               
               
                 tissue samples collected from cancer patients. 
               
            
           
           
               
               
               
               
               
               
            
               
                 Symbol 
                 Refseq 
                 Chr 
                 Start 
                 End 
                 Description 
               
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 AKAP17A 
                 NR_027383 
                 chrY 
                 1660485 
                 1671407 
                   
               
               
                 ASMT 
                 NM_001171038 
                 chrY 
                 1683940 
                 1711974 
                 acetylserotonin O- 
               
               
                   
                   
                   
                   
                   
                 methyltransferase 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 ASMTL 
                 NM_004192 
                 chrY 
                 1472031 
                 1521870 
                 N-acetylserotonin 
               
               
                   
                   
                   
                   
                   
                 O- 
               
               
                   
                   
                   
                   
                   
                 methyltransferase- 
               
               
                   
                   
                   
                   
                   
                 like protein 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 ASMTL-AS1 
                 NR_026711 
                 chrY 
                 1469423 
                 1484314 
               
               
                 CD99P1 
                 NR_033380 
                 chrY 
                 2477305 
                 2525270 
               
               
                 CRLF2 
                 NM_001012288 
                 chrY 
                 1264893 
                 1281616 
                 cytokine receptor- 
               
               
                   
                   
                   
                   
                   
                 like factor 2 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 DDX11L16 
                 NR_110561 
                 chrY 
                 59358328 
                 59360854 
               
               
                 IL3RA 
                 NM_002183 
                 chrY 
                 1405508 
                 1451582 
                 interleukin-3 
               
               
                   
                   
                   
                   
                   
                 receptor subunit 
               
               
                   
                   
                   
                   
                   
                 alpha isoform 1 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 IL9R 
                 NM_002186 
                 chrY 
                 59330251 
                 59343488 
                 interleukin-9 
               
               
                   
                   
                   
                   
                   
                 receptor isoform 1 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 LINC00685 
                 NR_027231 
                 chrY 
                 231384 
                 232054 
               
               
                 MIR3690 
                 NR_037461 
                 chrY 
                 1362810 
                 1362885 
               
               
                 MIR6089 
                 NR_106737 
                 chrY 
                 2477231 
                 2477295 
               
               
                 P2RY8 
                 NM_178129 
                 chrY 
                 1531465 
                 1606037 
                 P2Y purinoceptor 
               
               
                   
                   
                   
                   
                   
                 8 
               
               
                 SLC25A6 
                 NM_001636 
                 chrY 
                 1455044 
                 1461039 
                 ADP/ATP 
               
               
                   
                   
                   
                   
                   
                 translocase 3 
               
               
                 SLTM 
                 NM_001013843 
                 chr15 
                 59171243 
                 59225852 
                 SAFB-like 
               
               
                   
                   
                   
                   
                   
                 transcription 
               
               
                   
                   
                   
                   
                   
                 modulator isoform 
               
               
                   
                   
                   
                   
                   
                 b 
               
               
                 ZBED1 
                 NM_004729 
                 chrY 
                 2354454 
                 2369008 
                 zinc finger BED 
               
               
                   
                   
                   
                   
                   
                 domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 
               
               
                   
                   
                   
                   
                   
                 1 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 10 
               
             
            
               
                   
               
               
                 The candidate reference loci for use with tissue samples collected from healthy 
               
               
                 subjects and patients with myocardial infarction (non-tumor disease). 
               
            
           
           
               
               
               
               
               
               
            
               
                 Symbol 
                 Refseq 
                 Chr 
                 Start 
                 End 
                 Description 
               
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 ABCB7 
                 NM_004299 
                 chrX 
                 74273006 
                 74376175 
                 ATP-binding cassette sub- 
               
               
                   
                   
                   
                   
                   
                 family B member 7, 
               
               
                   
                   
                   
                   
                   
                 mitochondrial isoform 1 
               
               
                 ABCD1 
                 NM_000033 
                 chrX 
                 152990322 
                 153010216 
                 ATP-binding cassette sub- 
               
               
                   
                   
                   
                   
                   
                 family D member 1 
               
               
                 ACE2 
                 NM_021804 
                 chrX 
                 15579155 
                 15620192 
                 angiotens in-converting 
               
               
                   
                   
                   
                   
                   
                 enzyme 2 precursor 
               
               
                 ACTRT1 
                 NM_138289 
                 chrX 
                 127184940 
                 127186382 
                 actin-related protein T1 
               
               
                 AKAP4 
                 NM_139289 
                 chrX 
                 49955419 
                 49965004 
                 A-kinase anchor protein 4 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 ALAS2 
                 NM_001037968 
                 chrX 
                 55035487 
                 55057497 
                 5-aminolevulinate synthase, 
               
               
                   
                   
                   
                   
                   
                 erythroid-specific, 
               
               
                   
                   
                   
                   
                   
                 mitochondrial isoform c 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 ALG13 
                 NM_001099922 
                 chrX 
                 110924345 
                 111003875 
                 putative bifunctional UDP- 
               
               
                   
                   
                   
                   
                   
                 N-acetylglucosamine 
               
               
                   
                   
                   
                   
                   
                 transferase and 
               
               
                   
                   
                   
                   
                   
                 deubiquitinase ALG13 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 AMELX 
                 NM_001142 
                 chrX 
                 11311532 
                 11318881 
                 amelogenin, X isoform 
               
               
                   
                   
                   
                   
                   
                 isoform 1 precursor 
               
               
                 AMELY 
                 NM_001143 
                 chrY 
                 6733958 
                 6742068 
                 amelogenin, Y isoform 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 AMER1 
                 NM_152424 
                 chrX 
                 63404996 
                 63425624 
                 APC membrane recruitment 
               
               
                   
                   
                   
                   
                   
                 protein 1 
               
               
                 AMOT 
                 NM_001113490 
                 chrX 
                 112018104 
                 112066354 
                 angiomotin isoform 1 
               
               
                 ANHX 
                 NM_001191054 
                 chr12 
                 133794897 
                 133812422 
                 anomalous homeobox 
               
               
                   
                   
                   
                   
                   
                 protein 
               
               
                 AP1S2 
                 NM_003916 
                 chrX 
                 15843928 
                 15873137 
                 AP-1 complex subunit 
               
               
                   
                   
                   
                   
                   
                 sigma-2 isoform 2 
               
               
                 APEX2 
                 NM_014481 
                 chrX 
                 55026755 
                 55034306 
                 DNA-(apurinic or 
               
               
                   
                   
                   
                   
                   
                 apyrimidinic site) lyase 2 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 APOO 
                 NR_026545 
                 chrX 
                 23851464 
                 23926057 
               
               
                 APOOL 
                 NM_198450 
                 chrX 
                 84258897 
                 84348323 
                 MICOS complex subunit 
               
               
                   
                   
                   
                   
                   
                 MIC27 precursor 
               
               
                 ARAF 
                 NM_001256197 
                 chrX 
                 47420498 
                 47425373 
                 serine/threonine-protein 
               
               
                   
                   
                   
                   
                   
                 kinase A-Raf isoform 3 
               
               
                 ARHGAP4 
                 NM_001666 
                 chrX 
                 153172829 
                 153191714 
                 rho GTPase-activating 
               
               
                   
                   
                   
                   
                   
                 protein 4 isoform 2 
               
               
                 ARHGEF6 
                 NM_004840 
                 chrX 
                 135747711 
                 135863503 
                 rho guanine nucleotide 
               
               
                   
                   
                   
                   
                   
                 exchange factor 6 
               
               
                 ARHGEF9 
                 NM_001173480 
                 chrX 
                 62854847 
                 62975031 
                 rho guanine nucleotide 
               
               
                   
                   
                   
                   
                   
                 exchange factor 9 isoform 3 
               
               
                 ARHGEF9-IT1 
                 NR_046803 
                 chrX 
                 62890075 
                 62891382 
               
               
                 ARMCX1 
                 NM_016608 
                 chrX 
                 100805513 
                 100809675 
                 armadillo repeat-containing 
               
               
                   
                   
                   
                   
                   
                 X-linked protein 1 
               
               
                 ARMCX4 
                 NR_028407 
                 chrX 
                 100673250 
                 100790975 
               
               
                 ARX 
                 NM_139058 
                 chrX 
                 25021812 
                 25034065 
                 homeobox protein ARX 
               
               
                 ATG4A 
                 NM_178270 
                 chrX 
                 107334898 
                 107397901 
                 cysteine protease ATG4A 
               
               
                   
                   
                   
                   
                   
                 isoform b 
               
               
                 ATP2B3 
                 NM_021949 
                 chrX 
                 152801579 
                 152848387 
                 plasma membrane calcium- 
               
               
                   
                   
                   
                   
                   
                 transporting ATPase 3 
               
               
                   
                   
                   
                   
                   
                 isoform 3a 
               
               
                 ATP7A 
                 NM_001282224 
                 chrX 
                 77166152 
                 77305892 
                 copper-transporting ATPase 
               
               
                   
                   
                   
                   
                   
                 1 isoform 2 
               
               
                 ATRX 
                 NM_000489 
                 chrX 
                 76760355 
                 77041755 
                 transcriptional regulator 
               
               
                   
                   
                   
                   
                   
                 ATRX isoform 1 
               
               
                 ATXN3L 
                 NM_001135995 
                 chrX 
                 13336767 
                 13338518 
                 putative ataxin-3-like protein 
               
               
                 AVPR2 
                 NR_027419 
                 chrX 
                 153167984 
                 153172620 
               
               
                 AWAT2 
                 NM_001002254 
                 chrX 
                 69260391 
                 69269788 
                 acyl-CoA wax alcohol 
               
               
                   
                   
                   
                   
                   
                 acyltransferase 2 
               
               
                 BEX1 
                 NM_018476 
                 chrX 
                 102317580 
                 102319168 
                 protein BEX 1 
               
               
                 BEX2 
                 NM_032621 
                 chrX 
                 102564273 
                 102565974 
                 protein BEX2 isoform 3 
               
               
                 BEX4 
                 NM_001127688 
                 chrX 
                 102470019 
                 102472128 
                 protein BEX4 
               
               
                 BEX5 
                 NM_001159560 
                 chrX 
                 101408678 
                 101410762 
                 protein BEX5 
               
               
                 BMP 15 
                 NM_005448 
                 chrX 
                 50653734 
                 50659641 
                 bone morphogenetic protein 
               
               
                   
                   
                   
                   
                   
                 15 precursor 
               
               
                 BRDTP1 
                 NR_003539 
                 chrX 
                 95592084 
                 95592901 
               
               
                 BRS3 
                 NM_001727 
                 chrX 
                 135570124 
                 135574598 
                 bombesin receptor subtype-3 
               
               
                 C1GALT1C1 
                 NM_001011551 
                 chrX 
                 119759528 
                 119764005 
                 C1GALT1-specific 
               
               
                   
                   
                   
                   
                   
                 chaperone 1 
               
               
                 CA5B 
                 NM_007220 
                 chrX 
                 15756411 
                 15805748 
                 carbonic anhydrase 5B, 
               
               
                   
                   
                   
                   
                   
                 mitochondrial precursor 
               
               
                 CA5BP1 
                 NR_026551 
                 chrX 
                 15693038 
                 15721474 
               
               
                 CAPN6 
                 NM_014289 
                 chrX 
                 110488326 
                 110513774 
                 calpain-6 
               
               
                 CCDC160 
                 NM_001101357 
                 chrX 
                 133371076 
                 133379808 
                 coiled-coil domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 160 
               
               
                 CCNB3 
                 NM_033670 
                 chrX 
                 50027539 
                 50094911 
                 G2/mitotic-specific cyclin- 
               
               
                   
                   
                   
                   
                   
                 B3 isoform 1 
               
               
                 CD40LG 
                 NM_000074 
                 chrX 
                 135730335 
                 135742549 
                 CD40 ligand 
               
               
                 CDK16 
                 NM_001170460 
                 chrX 
                 47082416 
                 47089394 
                 cyclin-dependent kinase 16 
               
               
                   
                   
                   
                   
                   
                 isoform 3 
               
               
                 CDR1 
                 NM_004065 
                 chrX 
                 139865424 
                 139866723 
                 cerebellar degeneration- 
               
               
                   
                   
                   
                   
                   
                 related antigen 1 
               
               
                 CDX4 
                 NM_005193 
                 chrX 
                 72667089 
                 72674421 
                 homeobox protein CDX-4 
               
               
                 CDY1 
                 NM_170723 
                 chrY 
                 27768263 
                 27770485 
                 testis-specific 
               
               
                   
                   
                   
                   
                   
                 chromodomain protein Y1 
               
               
                   
                   
                   
                   
                   
                 isoform a 
               
               
                 CDY1B 
                 NM_001003894 
                 chrY 
                 27768263 
                 27770485 
                 testis-specific 
               
               
                   
                   
                   
                   
                   
                 chromodomain protein Y1 
               
               
                   
                   
                   
                   
                   
                 isoform a 
               
               
                 CDY2A 
                 NM_004825 
                 chrY 
                 20137666 
                 20139626 
                 testis-specific 
               
               
                   
                   
                   
                   
                   
                 chromodomain protein Y2 
               
               
                 CDY2B 
                 NM_001001722 
                 chrY 
                 20137667 
                 20139627 
                 testis-specific 
               
               
                   
                   
                   
                   
                   
                 chromodomain protein Y2 
               
               
                 CENPI 
                 NM_006733 
                 chrX 
                 100354797 
                 100417978 
                 centromere protein I 
               
               
                 CENPVP1 
                 NR_033772 
                 chrX 
                 51453924 
                 51455226 
               
               
                 CENPVP2 
                 NR_033773 
                 chrX 
                 51453924 
                 51455226 
               
               
                 CHDC2 
                 NM_173695 
                 chrX 
                 36065052 
                 36163187 
                 calponin homology domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 2 
               
               
                 CHMP1B2P 
                 NR_110646 
                 chrX 
                 79483987 
                 79590817 
               
               
                 CMC4 
                 NM_001018024 
                 chrX 
                 154289899 
                 154299547 
                 cx9C motif-containing 
               
               
                   
                   
                   
                   
                   
                 protein 4 
               
               
                 CSAG1 
                 NM_001102576 
                 chrX 
                 151903226 
                 151909518 
                 putative chondrosarcoma- 
               
               
                   
                   
                   
                   
                   
                 associated gene 1 protein 
               
               
                 CSAG3 
                 NM_001129828 
                 chrX 
                 151927733 
                 151928738 
                 chondrosarcoma-associated 
               
               
                   
                   
                   
                   
                   
                 gene 2/3 protein isoform b 
               
               
                 CSAG4 
                 NR_073432 
                 chrX 
                 151895977 
                 151903136 
               
               
                 CSPG4P1Y 
                 NR_001554 
                 chrY 
                 27629054 
                 27632852 
               
               
                 CT45A10 
                 NM_001291527 
                 chrX 
                 134945650 
                 134953901 
                 cancer/testis antigen family 
               
               
                   
                   
                   
                   
                   
                 45 member A-like 
               
               
                 CT45A7 
                 NM_001291543 
                 chrX 
                 134963218 
                 134971043 
                 cancer/testis antigen family 
               
               
                   
                   
                   
                   
                   
                 45 member A5-like 
               
               
                 CT45A8 
                 NM_001291535 
                 chrX 
                 134866213 
                 134874249 
                 cancer/testis antigen family 
               
               
                   
                   
                   
                   
                   
                 45 member A2-like 
               
               
                 CT45A9 
                 NM_001291540 
                 chrX 
                 134866213 
                 134874249 
                 cancer/testis antigen family 
               
               
                   
                   
                   
                   
                   
                 45 member A2-like 
               
               
                 CT47A12 
                 NM_001242922 
                 chrX 
                 120072555 
                 120075873 
                 cancer/testis antigen 47A 
               
               
                 CT55 
                 NM_017863 
                 chrX 
                 134290460 
                 134305751 
                 cancer/testis antigen 55 
               
               
                   
                   
                   
                   
                   
                 isoform 2 precursor 
               
               
                 CT83 
                 NM_001017978 
                 chrX 
                 115592852 
                 115594194 
                 kita-kyushu lung cancer 
               
               
                   
                   
                   
                   
                   
                 antigen 1 
               
               
                 CUL4B 
                 NM_001079872 
                 chrX 
                 119658445 
                 119694817 
                 cullin-4B isoform 2 
               
               
                 CXorf23 
                 NM_198279 
                 chrX 
                 19930979 
                 19988382 
                 uncharacterized protein 
               
               
                   
                   
                   
                   
                   
                 CXorf23 
               
               
                 CXorf51B 
                 NM_001244892 
                 chrX 
                 145895621 
                 145896249 
                 uncharacterized protein 
               
               
                   
                   
                   
                   
                   
                 LOC100133053 
               
               
                 CXorf58 
                 NM_152761 
                 chrX 
                 23926122 
                 23957624 
                 putative uncharacterized 
               
               
                   
                   
                   
                   
                   
                 protein CXorf58 isoform 1 
               
               
                 CXorf66 
                 NM_001013403 
                 chrX 
                 139037883 
                 139047677 
                 uncharacterized protein 
               
               
                   
                   
                   
                   
                   
                 CXorf66 precursor 
               
               
                 CXorf67 
                 NM_203407 
                 chrX 
                 51149766 
                 51151689 
                 uncharacterized protein 
               
               
                   
                   
                   
                   
                   
                 CXorf67 
               
               
                 CYBB 
                 NM_000397 
                 chrX 
                 37639269 
                 37672714 
                 cytochrome b-245 heavy 
               
               
                   
                   
                   
                   
                   
                 chain 
               
               
                 CYLC1 
                 NM_001271680 
                 chrX 
                 83116133 
                 83141708 
                 cylicin-1 isoform 2 
               
               
                 CYSLTR1 
                 NM_001282187 
                 chrX 
                 77526968 
                 77583188 
                 cysteinyl leukotriene 
               
               
                   
                   
                   
                   
                   
                 receptor 1 
               
               
                 DCX 
                 NM_178152 
                 chrX 
                 110537006 
                 110655460 
                 neuronal migration protein 
               
               
                   
                   
                   
                   
                   
                 doublecortin isoform b 
               
               
                 DDX11L1 
                 NR_046018 
                 chr1 
                 11873 
                 14409 
               
               
                 DDX11L16 
                 NR_110561 
                 chrY 
                 59358328 
                 59360854 
               
               
                 DDX11L5 
                 NR_051986 
                 chr9 
                 11986 
                 14525 
               
               
                 DDX26B-AS1 
                 NR_046740 
                 chrX 
                 134654007 
                 134654599 
               
               
                 DDX3Y 
                 NM_001122665 
                 chrY 
                 15016018 
                 15030439 
                 ATP-dependent RNA 
               
               
                   
                   
                   
                   
                   
                 helicase DDX3Y isoform 1 
               
               
                 DDX53 
                 NM_182699 
                 chrX 
                 23018077 
                 23020206 
                 DEAD box protein 53 
               
               
                 DIAPH2-AS1 
                 NR_125391 
                 chrX 
                 96783362 
                 96819534 
               
               
                 DKC1 
                 NR_110021 
                 chrX 
                 153991016 
                 154005964 
               
               
                 DLG3-AS1 
                 NR_109801 
                 chrX 
                 69672805 
                 69675844 
               
               
                 DMRTC1 
                 NM_033053 
                 chrX 
                 72091858 
                 72095622 
                 doublesex- and mab-3- 
               
               
                   
                   
                   
                   
                   
                 related transcription factor 
               
               
                   
                   
                   
                   
                   
                 C1 
               
               
                 DMRTC1B 
                 NM_001080851 
                 chrX 
                 72091858 
                 72095622 
                 doublesex- and mab-3- 
               
               
                   
                   
                   
                   
                   
                 related transcription factor 
               
               
                   
                   
                   
                   
                   
                 C1 
               
               
                 DUSP21 
                 NM_022076 
                 chrX 
                 44703248 
                 44704134 
                 dual specificity protein 
               
               
                   
                   
                   
                   
                   
                 phosphatase 21 
               
               
                 DUSP9 
                 NM_001395 
                 chrX 
                 152907896 
                 152916781 
                 dual specificity protein 
               
               
                   
                   
                   
                   
                   
                 phosphatase 9 
               
               
                 EDA2R 
                 NM_001242310 
                 chrX 
                 65815481 
                 65835872 
                 tumor necrosis factor 
               
               
                   
                   
                   
                   
                   
                 receptor superfamily 
               
               
                   
                   
                   
                   
                   
                 member 27 isoform 2 
               
               
                 EGFL6 
                 NM_015507 
                 chrX 
                 13587693 
                 13651694 
                 epidermal growth factor-like 
               
               
                   
                   
                   
                   
                   
                 protein 6 isoform 1 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 EIF1AX 
                 NM_001412 
                 chrX 
                 20142635 
                 20159966 
                 eukaryotic translation 
               
               
                   
                   
                   
                   
                   
                 initiation factor 1A, X- 
               
               
                   
                   
                   
                   
                   
                 chromosomal 
               
               
                 EIF1AX-AS1 
                 NR_046592 
                 chrX 
                 20158085 
                 20158562 
               
               
                 ELK1 
                 NM_001114123 
                 chrX 
                 47494918 
                 47510003 
                 ETS domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein Elk-1 isoform a 
               
               
                 ERCC6L 
                 NM_017669 
                 chrX 
                 71424506 
                 71458858 
                 DNA excision repair protein 
               
               
                   
                   
                   
                   
                   
                 ERCC-6-like 
               
               
                 ESX1 
                 NM_153448 
                 chrX 
                 103494718 
                 103499599 
                 homeobox protein ESX1 
               
               
                 FAM120C 
                 NM_017848 
                 chrX 
                 54094835 
                 54209691 
                 constitutive coactivator of 
               
               
                   
                   
                   
                   
                   
                 PPAR-gamma-like protein 2 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 FAM122B 
                 NM_001166599 
                 chrX 
                 133903595 
                 133931185 
                 protein FAM122B isoform 2 
               
               
                 FAM122C 
                 NM_001170781 
                 chrX 
                 133941222 
                 133945211 
                 protein FAM122C isoform 4 
               
               
                 FAM133A 
                 NM_173698 
                 chrX 
                 92929011 
                 92967273 
                 protein FAM133A 
               
               
                 FAM156A 
                 NM_001242489 
                 chrX 
                 52976463 
                 53024651 
                 protein 
               
               
                   
                   
                   
                   
                   
                 FAM156A/FAM156B 
               
               
                 FAM156B 
                 NM_001099684 
                 chrX 
                 52976463 
                 52985629 
                 protein 
               
               
                   
                   
                   
                   
                   
                 FAM156A/FAM156B 
               
               
                 FAM197Y2 
                 NR_001553 
                 chrY 
                 9316661 
                 9322263 
               
               
                 FAM197Y5 
                 NR_046300 
                 chrY 
                 9316661 
                 9322263 
               
               
                 FAM199X 
                 NM_207318 
                 chrX 
                 103411155 
                 103440582 
                 protein FAM199X 
               
               
                 FAM223A 
                 NR_027401 
                 chrX 
                 153799478 
                 153800188 
               
               
                 FAM223B 
                 NR_027402 
                 chrX 
                 153860738 
                 153861448 
               
               
                 FAM224A 
                 NR_002161 
                 chrY 
                 20488418 
                 20492712 
               
               
                 FAM224B 
                 NR_002160 
                 chrY 
                 20488439 
                 20492736 
               
               
                 FAM226A 
                 NR_026595 
                 chrX 
                 72161567 
                 72163589 
               
               
                 FAM226B 
                 NR_026594 
                 chrX 
                 72161567 
                 72163589 
               
               
                 FAM230C 
                 NR_027278 
                 chrUn_gl000212 
                 24048 
                 60768 
               
               
                 FAM41AY1 
                 NR_028083 
                 chrY 
                 20551155 
                 20566932 
               
               
                 FAM41AY2 
                 NR_028084 
                 chrY 
                 20551155 
                 20566932 
               
               
                 FAM46D 
                 NM_001170574 
                 chrX 
                 79591002 
                 79700810 
                 protein FAM46D 
               
               
                 FAM47C 
                 NM_001013736 
                 chrX 
                 37026431 
                 37029739 
                 putative protein FAM47C 
               
               
                 FAM58A 
                 NM_152274 
                 chrX 
                 152853382 
                 152864632 
                 cyclin-related protein 
               
               
                   
                   
                   
                   
                   
                 FAM58A isoform 1 
               
               
                 FAM9C 
                 NM_174901 
                 chrX 
                 13053735 
                 13062917 
                 protein FAM9C 
               
               
                 FATE1 
                 NM_033085 
                 chrX 
                 150884507 
                 150891664 
                 fetal and adult testis- 
               
               
                   
                   
                   
                   
                   
                 expressed transcript protein 
               
               
                 FGD1 
                 NM_004463 
                 chrX 
                 54471886 
                 54522599 
                 FYVE, RhoGEF and PH 
               
               
                   
                   
                   
                   
                   
                 domain-containing protein 1 
               
               
                 FGF13-AS1 
                 NR_038405 
                 chrX 
                 137794268 
                 137798763 
               
               
                 FGF16 
                 NM_003868 
                 chrX 
                 76709646 
                 76712013 
                 fibroblast growth factor 16 
               
               
                 FIRRE 
                 NR_026975 
                 chrX 
                 130836677 
                 130964671 
               
               
                 FLJ43315 
                 NR_033856 
                 chrUn_gl000211 
                 48502 
                 93165 
               
               
                 FLJ43681 
                 NR_029406 
                 chr17 
                 81174665 
                 81188573 
               
               
                 FMR1NB 
                 NM_152578 
                 chrX 
                 147062848 
                 147108187 
                 fragile X mental retardation 
               
               
                   
                   
                   
                   
                   
                 1 neighbor protein 
               
               
                 FRMD7 
                 NM_194277 
                 chrX 
                 131211020 
                 131262050 
                 FERM domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 7 
               
               
                 FRMD8P1 
                 NR_033742 
                 chrX 
                 64770501 
                 64772301 
               
               
                 FRMPD3 
                 NM_032428 
                 chrX 
                 106765679 
                 106848474 
                 FERM and PDZ domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 3 
               
               
                 FRMPD3-AS1 
                 NR_046750 
                 chrX 
                 106756212 
                 106789051 
               
               
                 FTH1P18 
                 NM_001271682 
                 chrX 
                 37060954 
                 37061867 
                 ferritin, heavy polypeptide- 
               
               
                   
                   
                   
                   
                   
                 like 18 
               
               
                 FTHL17 
                 NM_031894 
                 chrX 
                 31089357 
                 31090170 
                 ferritin heavy polypeptide- 
               
               
                   
                   
                   
                   
                   
                 like 17 
               
               
                 GABRQ 
                 NM_018558 
                 chrX 
                 151806636 
                 151821825 
                 gamma-aminobutyric acid 
               
               
                   
                   
                   
                   
                   
                 receptor subunit theta 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 GAGE12B 
                 NM_001127345 
                 chrX 
                 49306370 
                 49313636 
                 G antigen 12B/C/D/E 
               
               
                 GAGE12F 
                 NM_001098405 
                 chrX 
                 49306301 
                 49313700 
                 G antigen 12F 
               
               
                 GAGE12G 
                 NM_001098409 
                 chrX 
                 49335002 
                 49342360 
                 G antigen 12G 
               
               
                 GAGE12I 
                 NM_001477 
                 chrX 
                 49335064 
                 49342360 
                 G antigen 12I 
               
               
                 GAGE12J 
                 NM_001098406 
                 chrX 
                 49178508 
                 49294588 
                 G antigen 12J 
               
               
                 GAGE13 
                 NM_001098412 
                 chrX 
                 49188080 
                 49294588 
                 G antigen 13 
               
               
                 GAGE2B 
                 NM_001098411 
                 chrX 
                 49235707 
                 49242997 
                 G antigen 2B/2C 
               
               
                 GAGE2C 
                 NM_001472 
                 chrX 
                 49207148 
                 49223953 
                 G antigen 2B/2C 
               
               
                 GAGE2D 
                 NM_001098407 
                 chrX 
                 49207115 
                 49214420 
                 G antigen 2D 
               
               
                 GAGE2E 
                 NM_001127200 
                 chrX 
                 49207159 
                 49214420 
                 G antigen 2E 
               
               
                 GAGE4 
                 NM_001474 
                 chrX 
                 49216648 
                 49223939 
                 G antigen 4 
               
               
                 GAGE5 
                 NM_001475 
                 chrX 
                 49216656 
                 49223943 
                 G antigen 5 
               
               
                 GAGE6 
                 NM_001476 
                 chrX 
                 49325479 
                 49332807 
                 G antigen 6 
               
               
                 GAGE7 
                 NM_021123 
                 chrX 
                 49216677 
                 49223939 
                 G antigen 12G 
               
               
                 GAGE8 
                 NM_012196 
                 chrX 
                 49207159 
                 49214420 
                 G antigen 2D 
               
               
                 GK 
                 NM_001128127 
                 chrX 
                 30671475 
                 30749577 
                 glycerol kinase isoform c 
               
               
                 GLA 
                 NM_000169 
                 chrX 
                 100652778 
                 100663001 
                 alpha-galactosidase A 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 GLRA4 
                 NM_001172285 
                 chrX 
                 102973501 
                 102983552 
                 glycine receptor subunit 
               
               
                   
                   
                   
                   
                   
                 alpha-4 isoform 2 precursor 
               
               
                 GLUD2 
                 NM_012084 
                 chrX 
                 120181461 
                 120183796 
                 glutamate dehydrogenase 2, 
               
               
                   
                   
                   
                   
                   
                 mitochondrial precursor 
               
               
                 GNL3L 
                 NM_001184819 
                 chrX 
                 54556643 
                 54593720 
                 guanine nucleotide-binding 
               
               
                   
                   
                   
                   
                   
                 protein-like 3-like protein 
               
               
                 GOLGA2P2Y 
                 NR_001555 
                 chrY 
                 27601457 
                 27606322 
               
               
                 GOLGA2P3Y 
                 NR_002195 
                 chrY 
                 27601457 
                 27606322 
               
               
                 GPC3 
                 NM_004484 
                 chrX 
                 132669775 
                 133119673 
                 glypican-3 isoform 2 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 GPC4 
                 NM_001448 
                 chrX 
                 132435063 
                 132549205 
                 glypican-4 precursor 
               
               
                 GPR101 
                 NM_054021 
                 chrX 
                 136112306 
                 136113833 
                 probable G-protein coupled 
               
               
                   
                   
                   
                   
                   
                 receptor 101 
               
               
                 GPR112 
                 NM_153834 
                 chrX 
                 135383121 
                 135499047 
                 probable G-protein coupled 
               
               
                   
                   
                   
                   
                   
                 receptor 112 
               
               
                 GPR143 
                 NM_000273 
                 chrX 
                 9693452 
                 9734005 
                 G-protein coupled receptor 
               
               
                   
                   
                   
                   
                   
                 143 
               
               
                 GPR174 
                 NM_032553 
                 chrX 
                 78426468 
                 78427726 
                 probable G-protein coupled 
               
               
                   
                   
                   
                   
                   
                 receptor 174 
               
               
                 GRPR 
                 NM_005314 
                 chrX 
                 16141423 
                 16171641 
                 gastrin-releasing peptide 
               
               
                   
                   
                   
                   
                   
                 receptor 
               
               
                 GS1-600G8.3 
                 NR_046087 
                 chrX 
                 13328770 
                 13338052 
               
               
                 GSPT2 
                 NM_018094 
                 chrX 
                 51486480 
                 51489326 
                 eukaryotic peptide chain 
               
               
                   
                   
                   
                   
                   
                 release factor GTP-binding 
               
               
                   
                   
                   
                   
                   
                 subunit ERF3B 
               
               
                 GTPBP6 
                 NM_012227 
                 chrY 
                 171416 
                 180887 
                 putative GTP-binding 
               
               
                   
                   
                   
                   
                   
                 protein 6 
               
               
                 GUCY2F 
                 NM_001522 
                 chrX 
                 108616134 
                 108725285 
                 retinal guanylyl cyclase 2 
               
               
                 GYG2P1 
                 NR_033667 
                 chrY 
                 14517914 
                 14533389 
               
               
                 HCCS 
                 NM_005333 
                 chrX 
                 11129405 
                 11141204 
                 cytochrome c-type heme 
               
               
                   
                   
                   
                   
                   
                 lyase 
               
               
                 HCFC1 
                 NM_005334 
                 chrX 
                 153213007 
                 153236819 
                 host cell factor 1 
               
               
                 HCFC1-AS1 
                 NR_046608 
                 chrX 
                 153234215 
                 153235542 
               
               
                 HDAC8 
                 NM_001166420 
                 chrX 
                 71787431 
                 71792953 
                 histone deacetylase 8 
               
               
                   
                   
                   
                   
                   
                 isoform 4 
               
               
                 HDHD1 
                 NM_001178135 
                 chrX 
                 6975626 
                 7066231 
                 pseudouridine-5′- 
               
               
                   
                   
                   
                   
                   
                 monophosphatase isoform c 
               
               
                 HEPH 
                 NM_001282141 
                 chrX 
                 65384071 
                 65487230 
                 hephaestin isoform d 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 HLA-DRB3 
                 NM_022555 
                 chr6_cox_hap2 
                 3934126 
                 3947195 
                 major histocompatibility 
               
               
                   
                   
                   
                   
                   
                 complex, class II, DR beta 3 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 HLA-DRB4 
                 NM_021983 
                 chr6_ssto_hap7 
                 3850433 
                 3865402 
                 major histocompatibility 
               
               
                   
                   
                   
                   
                   
                 complex, class II, DR beta 4 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 HMGB3 
                 NM_001301231 
                 chrX 
                 150148980 
                 150159248 
                 high mobility group protein 
               
               
                   
                   
                   
                   
                   
                 B3 isoform b 
               
               
                 HNKNPH2 
                 NM_019597 
                 chrX 
                 100663120 
                 100669128 
                 heterogeneous nuclear 
               
               
                   
                   
                   
                   
                   
                 ribonucleoprotein H2 
               
               
                 HPRT1 
                 NM_000194 
                 chrX 
                 133594174 
                 133634698 
                 hypoxanthine-guanine 
               
               
                   
                   
                   
                   
                   
                 phosphoribosyltransferase 
               
               
                 HS6ST2-AS1 
                 NR_046691 
                 chrX 
                 131801669 
                 131803915 
               
               
                 HSD17B10 
                 NM_004493 
                 chrX 
                 53458205 
                 53461323 
                 3-hydroxyacyl-CoA 
               
               
                   
                   
                   
                   
                   
                 dehydrogenase type-2 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 HTATSF1 
                 NM_014500 
                 chrX 
                 135579670 
                 135594503 
                 HIV Tat-specific factor 1 
               
               
                 HYDIN2 
                 NR_103556 
                 chr1_gl000192_random 
                 132568 
                 407510 
               
               
                 HYPM 
                 NM_012274 
                 chrX 
                 37850069 
                 37850570 
                 huntingtin-interacting 
               
               
                   
                   
                   
                   
                   
                 protein M 
               
               
                 IDH3G 
                 NM_004135 
                 chrX 
                 153051220 
                 153059978 
                 isocitrate dehydrogenase 
               
               
                   
                   
                   
                   
                   
                 [NAD] subunit gamma, 
               
               
                   
                   
                   
                   
                   
                 mitochondrial isoform a 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 IGBP1 
                 NM_001551 
                 chrX 
                 69353317 
                 69386173 
                 immunoglobulin-binding 
               
               
                   
                   
                   
                   
                   
                 protein 1 
               
               
                 INE1 
                 NR_024616 
                 chrX 
                 47064246 
                 47065254 
               
               
                 INE2 
                 NR_002725 
                 chrX 
                 15803838 
                 15805712 
               
               
                 IQSEC2 
                 NM_015075 
                 chrX 
                 53262057 
                 53310796 
                 IQ motif and SEC7 domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 2 isoform 
               
               
                   
                   
                   
                   
                   
                 2 
               
               
                 IRAK1 
                 NM_001025243 
                 chrX 
                 153275956 
                 153285342 
                 interleukin-1 receptor- 
               
               
                   
                   
                   
                   
                   
                 associated kinase 1 isoform 
               
               
                   
                   
                   
                   
                   
                 3 
               
               
                 ITIH6 
                 NM_198510 
                 chrX 
                 54775331 
                 54824673 
                 inter-alpha-trypsin inhibitor 
               
               
                   
                   
                   
                   
                   
                 heavy chain H6 precursor 
               
               
                 JADE3 
                 NM_014735 
                 chrX 
                 46771867 
                 46920641 
                 protein Jade-3 
               
               
                 KANTR 
                 NR_110456 
                 chrX 
                 53123338 
                 53173249 
               
               
                 KCNE1L 
                 NM_012282 
                 chrX 
                 108866928 
                 108868393 
                 potassium voltage-gated 
               
               
                   
                   
                   
                   
                   
                 channel subfamily E 
               
               
                   
                   
                   
                   
                   
                 member 1-like protein 
               
               
                 KDM5C 
                 NM_001282622 
                 chrX 
                 53220502 
                 53254604 
                 lysine-specific demethylase 
               
               
                   
                   
                   
                   
                   
                 5C isoform 3 
               
               
                 KDM6A 
                 NM_001291421 
                 chrX 
                 44732420 
                 44971857 
                 lysine-specific demethylase 
               
               
                   
                   
                   
                   
                   
                 6A isoform 6 
               
               
                 KIAA1210 
                 NM_020721 
                 chrX 
                 118212597 
                 118284542 
                 uncharacterized protein 
               
               
                   
                   
                   
                   
                   
                 KIAA1210 
               
               
                 KIAA2022 
                 NM_001008537 
                 chrX 
                 73952690 
                 74145287 
                 protein KIAA2022 
               
               
                 KIR2DL2 
                 NM_014219 
                 chr19_gl000209_random 
                 21910 
                 36449 
                 killer cell immunoglobulin- 
               
               
                   
                   
                   
                   
                   
                 like receptor 2DL2 precursor 
               
               
                 KIR2DL5A 
                 NM_020535 
                 chr19_gl000209_random 
                 86690 
                 96155 
                 killer cell immunoglobulin- 
               
               
                   
                   
                   
                   
                   
                 like receptor 2DL5A 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 KIR2DL5B 
                 NM_001018081 
                 chr19_gl000209_random 
                 86745 
                 96246 
                 killer cell immunoglobulin- 
               
               
                   
                   
                   
                   
                   
                 like receptor 2DL5B 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 KIR2DS1 
                 NMJH4512 
                 chr19_gl000209_random 
                 115098 
                 129113 
                 killer cell immunoglobulin- 
               
               
                   
                   
                   
                   
                   
                 like receptor 2DS1 precursor 
               
               
                 KIR2DS2 
                 NM_001291695 
                 chr19_gl000209_random 
                 131432 
                 145743 
                 killer cell immunoglobulin- 
               
               
                   
                   
                   
                   
                   
                 like receptor 2DS2 isoform b 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 KIR2DS3 
                 NM_012313 
                 chr19_gl000209_random 
                 98134 
                 112667 
                 killer cell immunoglobulin- 
               
               
                   
                   
                   
                   
                   
                 like receptor 2DS3 precursor 
               
               
                 KIR2DS5 
                 NM_014513 
                 chr19_gl000209_random 
                 98111 
                 113132 
                 killer cell immunoglobulin- 
               
               
                   
                   
                   
                   
                   
                 like receptor 2DS5 precursor 
               
               
                 KIR3DS1 
                 NM_001083539 
                 chr19_gl000209_random 
                 70070 
                 84658 
                 killer cell immunoglobulin- 
               
               
                   
                   
                   
                   
                   
                 like receptor 3DS1 isoform 1 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 KLF8 
                 NM_001159296 
                 chrX 
                 56258869 
                 56314322 
                 Krueppel-like factor 8 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 KLHL34 
                 NM_153270 
                 chrX 
                 21673608 
                 21676448 
                 kelch-like protein 34 
               
               
                 KRBOX4 
                 NM_017776 
                 chrX 
                 46306623 
                 46334074 
                 KRAB domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 4 isoform 2 
               
               
                 LANCL3 
                 NM_198511 
                 chrX 
                 37430821 
                 37536750 
                 lanC-like protein 3 isoform 1 
               
               
                 LAS1L 
                 NM_001170649 
                 chrX 
                 64732461 
                 64754686 
                 ribosomal biogenesis protein 
               
               
                   
                   
                   
                   
                   
                 LAS1L isoform 2 
               
               
                 LHFPL1 
                 NM_178175 
                 chrX 
                 111873878 
                 111923375 
                 lipoma HMGIC fusion 
               
               
                   
                   
                   
                   
                   
                 partner-like 1 protein 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 LINC00087 
                 NR_024493 
                 chrX 
                 134229014 
                 134232733 
               
               
                 LINC00266-3 
                 NR_109817 
                 chrUn_gl000227 
                 66129 
                 74245 
               
               
                 LINC00269 
                 NR_103715 
                 chrX 
                 68399399 
                 68429767 
               
               
                 LINC00278 
                 NR_046502 
                 chrY 
                 2871036 
                 2970313 
               
               
                 LINC00280 
                 NR_046505 
                 chrY 
                 6225259 
                 6229454 
               
               
                 LINC00629 
                 NR_038998 
                 chrX 
                 133684053 
                 133694428 
               
               
                 LINC00630 
                 NR_038988 
                 chrX 
                 102024094 
                 102140338 
               
               
                 LINC00632 
                 NR_028344 
                 chrX 
                 139791923 
                 139796996 
               
               
                 LINC00633 
                 NR_033941 
                 chrX 
                 134252881 
                 134254405 
               
               
                 LINC00684 
                 NR_120499 
                 chrX 
                 72158002 
                 72158798 
               
               
                 LINC00685 
                 NR_027231 
                 chrY 
                 231384 
                 232054 
               
               
                 LINC00850 
                 NR_109813 
                 chrX 
                 148958632 
                 149008599 
               
               
                 LINC00889 
                 NR_026935 
                 chrX 
                 137696891 
                 137699799 
               
               
                 LINC00890 
                 NR_033974 
                 chrX 
                 110754889 
                 110765627 
               
               
                 LINC00891 
                 NR_034005 
                 chrX 
                 70917045 
                 70923256 
               
               
                 LINC00892 
                 NR_038461 
                 chrX 
                 135721701 
                 135724588 
               
               
                 LINC00893 
                 NR_027455 
                 chrX 
                 148609131 
                 148621312 
               
               
                 LINC00894 
                 NR_027456 
                 chrX 
                 149106765 
                 149185018 
               
               
                 LINC01001 
                 NR_028326 
                 chr11 
                 126986 
                 131920 
               
               
                 LINC01186 
                 NR_110388 
                 chrX 
                 46185358 
                 46187109 
               
               
                 LINC01201 
                 NR_126350 
                 chrX 
                 130150442 
                 130192120 
               
               
                 LINC01203 
                 NR_045260 
                 chrX 
                 13353359 
                 13359944 
               
               
                 LINC01204 
                 NR_104644 
                 chrX 
                 45364632 
                 45386484 
               
               
                 LINC01278 
                 NR_015353 
                 chrX 
                 62646438 
                 62780873 
               
               
                 LINC01281 
                 NR_038968 
                 chrX 
                 39164209 
                 39186616 
               
               
                 LINC01282 
                 NR_110385 
                 chrX 
                 39226538 
                 39251028 
               
               
                 LINC01284 
                 NR_110382 
                 chrX 
                 50838681 
                 50914232 
               
               
                 LINC01285 
                 NR_110393 
                 chrX 
                 117973518 
                 118015977 
               
               
                 LINC01402 
                 NR_126557 
                 chrX 
                 119251551 
                 119253610 
               
               
                 LINC01420 
                 NR_015367 
                 chrX 
                 56755717 
                 56844004 
               
               
                 LINC01496 
                 NR_110654 
                 chrX 
                 51242760 
                 51250293 
               
               
                 LINC01545 
                 NR_046101 
                 chrX 
                 46746853 
                 46759139 
               
               
                 LINC01546 
                 NR_038428 
                 chrX 
                 3189860 
                 3202694 
               
               
                 LINC01560 
                 NR_126059 
                 chrX 
                 47342114 
                 47344626 
               
               
                 LOC100132304 
                 NR_120493 
                 chrX 
                 72158002 
                 72158798 
               
               
                 LOC100233156 
                 NR_037872 
                 chrUn_gl000218 
                 38785 
                 97454 
               
               
                 LOC100287728 
                 NR_103770 
                 chrX 
                 134254548 
                 134257529 
               
               
                 LOC100288778 
                 NR_028269 
                 chr12 
                 87983 
                 91263 
               
               
                 LOC100288814 
                 NM_001195081 
                 chrX 
                 9935397 
                 9936042 
                 uncharacterized protein 
               
               
                   
                   
                   
                   
                   
                 LOC100288814 
               
               
                 LOC100288966 
                 NM_001257362 
                 chrUn_gl000213 
                 108006 
                 139339 
                 uncharacterized protein 
               
               
                   
                   
                   
                   
                   
                 LOC100288966 
               
               
                 LOC100506790 
                 NR_104652 
                 chrX 
                 134530353 
                 134531672 
               
               
                 LOC100507412 
                 NR_038958 
                 chrUn_gl000220 
                 97128 
                 126696 
               
               
                 LOC100652931 
                 NR_104151 
                 chrY 
                 24462824 
                 24466531 
               
               
                 LOC101927476 
                 NR_110386 
                 chrX 
                 40122169 
                 40146974 
               
               
                 LOC101927501 
                 NR_110387 
                 chrX 
                 43036242 
                 43085847 
               
               
                 LOC101927830 
                 NR_109985 
                 chrX 
                 154696200 
                 154723771 
               
               
                 LOC101928128 
                 NR_110651 
                 chrX 
                 84465711 
                 84474295 
               
               
                 LOC101928201 
                 NR_110390 
                 chrX 
                 4545240 
                 4551613 
               
               
                 LOC101928259 
                 NR_110391 
                 chrX 
                 71908798 
                 71932190 
               
               
                 LOC101928335 
                 NR_110395 
                 chrX 
                 107137826 
                 107179210 
               
               
                 LOC101928336 
                 NR_110396 
                 chrX 
                 118425491 
                 118469573 
               
               
                 LOC101928358 
                 NR_110652 
                 chrX 
                 107979769 
                 107982133 
               
               
                 LOC101928437 
                 NR_110399 
                 chrX 
                 112285954 
                 112763885 
               
               
                 LOC101928495 
                 NR_110409 
                 chrX 
                 125243744 
                 125249545 
               
               
                 LOC101928564 
                 NR_104642 
                 chrX 
                 36011397 
                 36019767 
               
               
                 LOC101929148 
                 NR_110413 
                 chrY 
                 24585086 
                 24630861 
               
               
                 LOC102724558 
                 NR_120328 
                 chr1_gl000192_random 
                 429709 
                 468683 
               
               
                 LOC104798195 
                 NR_126564 
                 chrX 
                 15621003 
                 15639607 
               
               
                 LOC158960 
                 NR_103768 
                 chrX 
                 153652722 
                 153656825 
               
               
                 LOC283788 
                 NR_027436 
                 chrUn_gl000219 
                 56348 
                 99642 
               
               
                 LOC389831 
                 NM_001242480 
                 chr7_gl000195_random 
                 42937 
                 86719 
                 uncharacterized protein 
               
               
                   
                   
                   
                   
                   
                 LOC389831 
               
               
                 LOC389834 
                 NR_027420 
                 chrUn_gl000218 
                 46844 
                 55049 
               
               
                 LOC389895 
                 NM_001271560 
                 chrX 
                 139173825 
                 139175070 
                 uncharacterized protein 
               
               
                   
                   
                   
                   
                   
                 LOC389895 
               
               
                 LOC389906 
                 NR_034031 
                 chrX 
                 3735575 
                 3761935 
               
               
                 LOC392452 
                 NR_102268 
                 chrX 
                 45590576 
                 45591246 
               
               
                 LOC401585 
                 NR_125365 
                 chrX 
                 45707508 
                 45710920 
               
               
                 LOC729609 
                 NR_024440 
                 chrX 
                 20004934 
                 20007897 
               
               
                 LONRF3 
                 NR_110311 
                 chrX 
                 118108576 
                 118152318 
               
               
                 MAFIP 
                 NR_046442 
                 chr4_gl000194_random 
                 61659 
                 115073 
               
               
                 MAGEA12 
                 NM_005367 
                 chrX 
                 151899292 
                 151903184 
                 melanoma-associated 
               
               
                   
                   
                   
                   
                   
                 antigen 12 
               
               
                 MAGEA2 
                 NM_005361 
                 chrX 
                 151918386 
                 151922408 
                 melanoma-associated 
               
               
                   
                   
                   
                   
                   
                 antigen 1 
               
               
                 MAGEA2B 
                 NM_153488 
                 chrX 
                 151918403 
                 151920099 
                 melanoma-associated 
               
               
                   
                   
                   
                   
                   
                 antigen 2 
               
               
                 MAGEA3 
                 NM_005362 
                 chrX 
                 151934651 
                 151938240 
                 melanoma-associated 
               
               
                   
                   
                   
                   
                   
                 antigen 3 
               
               
                 MAGEA6 
                 NM_175868 
                 chrX 
                 151867244 
                 151870814 
                 melanoma-associated 
               
               
                   
                   
                   
                   
                   
                 antigen 6 
               
               
                 MAGEA8-AS1 
                 NR_102703 
                 chrX 
                 149007562 
                 149025779 
               
               
                 MAGEB1 
                 NM_002363 
                 chrX 
                 30261847 
                 30270155 
                 melanoma-associated 
               
               
                   
                   
                   
                   
                   
                 antigen B1 
               
               
                 MAGEB17 
                 NM_001277307 
                 chrX 
                 16185603 
                 16189516 
                 melanoma-associated 
               
               
                   
                   
                   
                   
                   
                 antigen B17 
               
               
                 MAGEB18 
                 NM_173699 
                 chrX 
                 26156459 
                 26158853 
                 melanoma-associated 
               
               
                   
                   
                   
                   
                   
                 antigen B18 
               
               
                 MAGEB2 
                 NM_002364 
                 chrX 
                 30233674 
                 30238206 
                 melanoma-associated 
               
               
                   
                   
                   
                   
                   
                 antigen B2 
               
               
                 MAGEB3 
                 NM_002365 
                 chrX 
                 30248552 
                 30255610 
                 melanoma-associated 
               
               
                   
                   
                   
                   
                   
                 antigen B3 
               
               
                 MAGEB4 
                 NM_002367 
                 chrX 
                 30260056 
                 30262308 
                 melanoma-associated 
               
               
                   
                   
                   
                   
                   
                 antigen B4 
               
               
                 MAGEB5 
                 NM_001271752 
                 chrX 
                 26234285 
                 26236387 
                 melanoma-associated 
               
               
                   
                   
                   
                   
                   
                 antigen B5 
               
               
                 MAGEB6 
                 NM_173523 
                 chrX 
                 26210556 
                 26213763 
                 melanoma-associated 
               
               
                   
                   
                   
                   
                   
                 antigen B6 
               
               
                 MAGEC2 
                 NM_016249 
                 chrX 
                 141290127 
                 141293076 
                 melanoma-associated 
               
               
                   
                   
                   
                   
                   
                 antigen C2 
               
               
                 MAGED2 
                 NM_014599 
                 chrX 
                 54834770 
                 54842448 
                 melanoma-associated 
               
               
                   
                   
                   
                   
                   
                 antigen D2 
               
               
                 MAGEE1 
                 NM_020932 
                 chrX 
                 75648045 
                 75651746 
                 melanoma-associated 
               
               
                   
                   
                   
                   
                   
                 antigen E1 
               
               
                 MAGEH1 
                 NM_014061 
                 chrX 
                 55478521 
                 55480001 
                 melanoma-associated 
               
               
                   
                   
                   
                   
                   
                 antigen H1 
               
               
                 MAOB 
                 NM_000898 
                 chrX 
                 43625856 
                 43741721 
                 amine oxidase [flavin- 
               
               
                   
                   
                   
                   
                   
                 containing] B 
               
               
                 MAP2K4P1 
                 NR_029423 
                 chrX 
                 72744110 
                 72782921 
               
               
                 MAP7D3 
                 NM_001173517 
                 chrX 
                 135295378 
                 135333738 
                 MAP7 domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 3 isoform 3 
               
               
                 MBTPS2 
                 NM_015884 
                 chrX 
                 21857655 
                 21903541 
                 membrane-bound 
               
               
                   
                   
                   
                   
                   
                 transcription factor site-2 
               
               
                   
                   
                   
                   
                   
                 protease 
               
               
                 MCTS1 
                 NM_001137554 
                 chrX 
                 119738551 
                 119755016 
                 malignant T-cell-amplified 
               
               
                   
                   
                   
                   
                   
                 sequence 1 isoform 2 
               
               
                 MED14OS 
                 NM_001289773 
                 chrX 
                 40594647 
                 40597953 
                 uncharacterized protein 
               
               
                   
                   
                   
                   
                   
                 LOC100873985 
               
               
                 MGC39584 
                 NR_038377 
                 chr4_gl000193_random 
                 49162 
                 88375 
               
               
                 MGC70870 
                 NR_003682 
                 chr17_gl000205_random 
                 116622 
                 119732 
               
               
                 MID1IP1 
                 NM_021242 
                 chrX 
                 38660684 
                 38665783 
                 mid1-interacting protein 1 
               
               
                 MID1IP1-AS1 
                 NR_046706 
                 chrX 
                 38660500 
                 38663136 
               
               
                 MID2 
                 NM_012216 
                 chrX 
                 107069083 
                 107174867 
                 probable E3 ubiquitin- 
               
               
                   
                   
                   
                   
                   
                 protein ligase MID2 isoform 
               
               
                   
                   
                   
                   
                   
                 1 
               
               
                 MIR105-1 
                 NR_029521 
                 chrX 
                 151560690 
                 151560771 
               
               
                 MIR105-2 
                 NR_029522 
                 chrX 
                 151562883 
                 151562964 
               
               
                 MIR106A 
                 NR_029523 
                 chrX 
                 133304227 
                 133304308 
               
               
                 MIR1277 
                 NR_031685 
                 chrX 
                 117520356 
                 117520434 
               
               
                 MIR1468 
                 NR_031567 
                 chrX 
                 63005881 
                 63005967 
               
               
                 MIR188 
                 NR_029708 
                 chrX 
                 49768108 
                 49768194 
               
               
                 MIR18B 
                 NR_029949 
                 chrX 
                 133304070 
                 133304141 
               
               
                 MIR19B2 
                 NR_029491 
                 chrX 
                 133303700 
                 133303796 
               
               
                 MIR20B 
                 NR_029950 
                 chrX 
                 133303838 
                 133303907 
               
               
                 MIR221 
                 NR_029635 
                 chrX 
                 45605584 
                 45605694 
               
               
                 MIR222 
                 NR_029636 
                 chrX 
                 45606420 
                 45606530 
               
               
                 MIR223 
                 NR_029637 
                 chrX 
                 65238711 
                 65238821 
               
               
                 MIR23C 
                 NR_037414 
                 chrX 
                 20035205 
                 20035305 
               
               
                 MIR325HG 
                 NR_110406 
                 chrX 
                 75878198 
                 76234957 
               
               
                 MIR362 
                 NR_029850 
                 chrX 
                 49773571 
                 49773635 
               
               
                 MIR363 
                 NR_029852 
                 chrX 
                 133303407 
                 133303482 
               
               
                 MIR374A 
                 NR_030785 
                 chrX 
                 73507120 
                 73507192 
               
               
                 MIR374B 
                 NR_030620 
                 chrX 
                 73438381 
                 73438453 
               
               
                 MIR374C 
                 NR_037511 
                 chrX 
                 73438383 
                 73438453 
               
               
                 MIR3978 
                 NR_039774 
                 chrX 
                 109325345 
                 109325446 
               
               
                 MIR421 
                 NR_030398 
                 chrX 
                 73438211 
                 73438296 
               
               
                 MIR424 
                 NR_029946 
                 chrX 
                 133680643 
                 133680741 
               
               
                 MIR4328 
                 NR_036258 
                 chrX 
                 78156690 
                 78156746 
               
               
                 MIR4329 
                 NR_036255 
                 chrX 
                 112023945 
                 112024016 
               
               
                 MIR450A1 
                 NR_029962 
                 chrX 
                 133674370 
                 133674461 
               
               
                 MIR450A2 
                 NR_030227 
                 chrX 
                 133674537 
                 133674637 
               
               
                 MIR450B 
                 NR_030587 
                 chrX 
                 133674214 
                 133674292 
               
               
                 MIR4536-1 
                 NR_039764 
                 chrX 
                 55477892 
                 55477953 
               
               
                 MIR4767 
                 NR_039924 
                 chrX 
                 7065900 
                 7065978 
               
               
                 MIR4769 
                 NR_039926 
                 chrX 
                 47446827 
                 47446904 
               
               
                 MIR500A 
                 NR_030224 
                 chrX 
                 49773038 
                 49773122 
               
               
                 MIR500B 
                 NR_036257 
                 chrX 
                 49775279 
                 49775358 
               
               
                 MIR501 
                 NR_030225 
                 chrX 
                 49774329 
                 49774413 
               
               
                 MIR502 
                 NR_030226 
                 chrX 
                 49779205 
                 49779291 
               
               
                 MIR503 
                 NR_030228 
                 chrX 
                 133680357 
                 133680428 
               
               
                 MIR503HG 
                 NR_024607 
                 chrX 
                 133677406 
                 133680660 
               
               
                 MIR505 
                 NR_030230 
                 chrX 
                 139006306 
                 139006390 
               
               
                 MIR514A1 
                 NR_030238 
                 chrX 
                 146360764 
                 146360862 
               
               
                 MIR514A2 
                 NR_030239 
                 chrX 
                 146366158 
                 146366246 
               
               
                 MIR514A3 
                 NR_030240 
                 chrX 
                 146366158 
                 146366246 
               
               
                 MIR532 
                 NR_030241 
                 chrX 
                 49767753 
                 49767844 
               
               
                 MIR542 
                 NR_030399 
                 chrX 
                 133675370 
                 133675467 
               
               
                 MIR545 
                 NR_030258 
                 chrX 
                 73506938 
                 73507044 
               
               
                 MIR6086 
                 NR_106734 
                 chrX 
                 13608410 
                 13608465 
               
               
                 MIR6089 
                 NR_106737 
                 chrY 
                 2477231 
                 2477295 
               
               
                 MIR6134 
                 NR_106750 
                 chrX 
                 28513671 
                 28513780 
               
               
                 MIR660 
                 NR_030397 
                 chrX 
                 49777848 
                 49777945 
               
               
                 MIR664B 
                 NR_049842 
                 chrX 
                 153996870 
                 153996931 
               
               
                 MIR6724-1 
                 NR_106782 
                 chrUn_gl000220 
                 148703 
                 148795 
               
               
                 MIR6724-2 
                 NR_128715 
                 chrUn_gl000220 
                 148703 
                 148795 
               
               
                 MIR6724-3 
                 NR_128716 
                 chrUn_gl000220 
                 148703 
                 148795 
               
               
                 MIR6724-4 
                 NR_128717 
                 chrUn_gl000220 
                 148703 
                 148795 
               
               
                 MIR676 
                 NR_037494 
                 chrX 
                 69242706 
                 69242773 
               
               
                 MIR6857 
                 NR_106916 
                 chrX 
                 53432604 
                 53432697 
               
               
                 MIR6858 
                 NR_106917 
                 chrX 
                 153678667 
                 153678734 
               
               
                 MIR6894 
                 NR_106954 
                 chrX 
                 53228070 
                 53228127 
               
               
                 MIR6895 
                 NR_106955 
                 chrX 
                 53224592 
                 53224670 
               
               
                 MIR718 
                 NR_031757 
                 chrX 
                 153285370 
                 153285440 
               
               
                 MIR766 
                 NR_030413 
                 chrX 
                 118780700 
                 118780811 
               
               
                 MIR767 
                 NR_030409 
                 chrX 
                 151561892 
                 151562001 
               
               
                 MIR8088 
                 NR_107055 
                 chrX 
                 52079698 
                 52079784 
               
               
                 MIR888 
                 NR_030592 
                 chrX 
                 145076301 
                 145076378 
               
               
                 MIR890 
                 NR_030589 
                 chrX 
                 145075792 
                 145075869 
               
               
                 MIR891A 
                 NR_030581 
                 chrX 
                 145109311 
                 145109390 
               
               
                 MIR891B 
                 NR_030590 
                 chrX 
                 145082570 
                 145082649 
               
               
                 MIR892A 
                 NR_030584 
                 chrX 
                 145078186 
                 145078261 
               
               
                 MIR892B 
                 NR_030593 
                 chrX 
                 145078715 
                 145078792 
               
               
                 MIR892C 
                 NR_106783 
                 chrX 
                 145074267 
                 145074344 
               
               
                 MIR92A2 
                 NR_029509 
                 chrX 
                 133303567 
                 133303642 
               
               
                 MIR934 
                 NR_030631 
                 chrX 
                 135633036 
                 135633119 
               
               
                 MIR98 
                 NR_029513 
                 chrX 
                 53583183 
                 53583302 
               
               
                 MIRLET7F2 
                 NR_029484 
                 chrX 
                 53584152 
                 53584235 
               
               
                 MORF4L2 
                 NM_001142424 
                 chrX 
                 102930425 
                 102941746 
                 mortality factor 4-like 
               
               
                   
                   
                   
                   
                   
                 protein 2 
               
               
                 MORF4L2- 
                 NR_038978 
                 chrX 
                 102942211 
                 102947484 
               
               
                 AS1 
               
               
                 MOSPD1 
                 NM_019556 
                 chrX 
                 134021661 
                 134049297 
                 motile sperm domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 1 
               
               
                 MPC1L 
                 NM_001195522 
                 chrX 
                 40482817 
                 40483391 
                 mitochondrial pyruvate 
               
               
                   
                   
                   
                   
                   
                 carrier 1-like protein 
               
               
                 MSN 
                 NM_002444 
                 chrX 
                 64887510 
                 64961793 
                 moesin 
               
               
                 MTMR8 
                 NM_017677 
                 chrX 
                 63487960 
                 63615333 
                 myotubularin-related protein 
               
               
                   
                   
                   
                   
                   
                 8 
               
               
                 MTRNR2L10 
                 NM_001190708 
                 chrX 
                 55207823 
                 55208944 
                 humanin-like 10 
               
               
                 MXRA5 
                 NM_015419 
                 chrX 
                 3226608 
                 3264684 
                 matrix-remodeling- 
               
               
                   
                   
                   
                   
                   
                 associated protein 5 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 NAA10 
                 NM_001256120 
                 chrX 
                 153195279 
                 153200607 
                 N-alpha-acetyltransferase 10 
               
               
                   
                   
                   
                   
                   
                 isoform 3 
               
               
                 NAP1L2 
                 NM_021963 
                 chrX 
                 72432136 
                 72434710 
                 nucleosome assembly 
               
               
                   
                   
                   
                   
                   
                 protein 1-like 2 
               
               
                 NAP1L3 
                 NM_004538 
                 chrX 
                 92925924 
                 92928682 
                 nucleosome assembly 
               
               
                   
                   
                   
                   
                   
                 protein 1-like 3 
               
               
                 NAP1L6 
                 NR_027291 
                 chrX 
                 72345875 
                 72347919 
               
               
                 NDP 
                 NM_000266 
                 chrX 
                 43808023 
                 43832921 
                 norrin precursor 
               
               
                 NDUFA1 
                 NM_004541 
                 chrX 
                 119005733 
                 119010629 
                 NADH dehydrogenase 
               
               
                   
                   
                   
                   
                   
                 [ubiquinone] 1 alpha 
               
               
                   
                   
                   
                   
                   
                 subcomplex subunit 1 
               
               
                 NDUFB11 
                 NM_001135998 
                 chrX 
                 47001614 
                 47004609 
                 NADH dehydrogenase 
               
               
                   
                   
                   
                   
                   
                 [ubiquinone] 1 beta 
               
               
                   
                   
                   
                   
                   
                 subcomplex subunit 11, 
               
               
                   
                   
                   
                   
                   
                 mitochondrial isoform 2 
               
               
                 NGFRAP1 
                 NM_014380 
                 chrX 
                 102632108 
                 102633092 
                 protein BEX3 isoform b 
               
               
                 NHS-AS1 
                 NR_046632 
                 chrX 
                 17570469 
                 17577248 
               
               
                 NKAPP1 
                 NR_027131 
                 chrX 
                 119370308 
                 119379122 
               
               
                 NKRF 
                 NM_001173488 
                 chrX 
                 118722299 
                 118727113 
                 NF-kappa-B-repressing 
               
               
                   
                   
                   
                   
                   
                 factor isoform 2 
               
               
                 NLGN4Y-AS1 
                 NR_046504 
                 chrY 
                 16905521 
                 16915913 
               
               
                 NOX1 
                 NM_007052 
                 chrX 
                 100098312 
                 100129334 
                 NADPH oxidase 1 isoform 1 
               
               
                 NUDT10 
                 NM_153183 
                 chrX 
                 51075082 
                 51080377 
                 diphosphoinositol 
               
               
                   
                   
                   
                   
                   
                 polyphosphate 
               
               
                   
                   
                   
                   
                   
                 phosphohydrolase 3-alpha 
               
               
                 NXF2 
                 NM_022053 
                 chrX 
                 101615315 
                 101694929 
                 nuclear RNA export factor 2 
               
               
                 NXF2B 
                 NM_001099686 
                 chrX 
                 101615315 
                 101694929 
                 nuclear RNA export factor 2 
               
               
                 NXF3 
                 NM_022052 
                 chrX 
                 102330749 
                 102348022 
                 nuclear RNA export factor 3 
               
               
                 NXF4 
                 NR_002216 
                 chrX 
                 101804892 
                 101826621 
               
               
                 NXT2 
                 NM_001242618 
                 chrX 
                 108780346 
                 108787927 
                 NTF2-related export protein 
               
               
                   
                   
                   
                   
                   
                 2 isoform 3 
               
               
                 OCRL 
                 NM_001587 
                 chrX 
                 128674251 
                 128726530 
                 inositol polyphosphate 5- 
               
               
                   
                   
                   
                   
                   
                 phosphatase OCRL-1 
               
               
                   
                   
                   
                   
                   
                 isoform b 
               
               
                 OTC 
                 NM_000531 
                 chrX 
                 38211735 
                 38280703 
                 ornithine 
               
               
                   
                   
                   
                   
                   
                 carbamoyltransferase, 
               
               
                   
                   
                   
                   
                   
                 mitochondrial precursor 
               
               
                 OTUD6A 
                 NM_207320 
                 chrX 
                 69282340 
                 69284029 
                 OTU domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 6A 
               
               
                 P2RY10 
                 NM_014499 
                 chrX 
                 78200828 
                 78217438 
                 putative P2Y purinoceptor 
               
               
                   
                   
                   
                   
                   
                 10 
               
               
                 PABPC1L2B- 
                 NR_110398 
                 chrX 
                 72300005 
                 72304474 
               
               
                 AS1 
               
               
                 PABPC5-AS1 
                 NR_110659 
                 chrX 
                 90669901 
                 90689998 
               
               
                 PAGE1 
                 NM_003785 
                 chrX 
                 49452053 
                 49460596 
                 P antigen family member 1 
               
               
                 PAGE3 
                 NR_033460 
                 chrX 
                 55284848 
                 55291165 
               
               
                 PAGE4 
                 NM_007003 
                 chrX 
                 49593905 
                 49598637 
                 P antigen family member 4 
               
               
                 PAGE5 
                 NM_130467 
                 chrX 
                 55246790 
                 55250541 
                 P antigen family member 5 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 PAK3 
                 NM_001128166 
                 chrX 
                 110187512 
                 110464173 
                 serine/threonine-protein 
               
               
                   
                   
                   
                   
                   
                 kinase PAK 3 isoform a 
               
               
                 PBDC1 
                 NM_001300888 
                 chrX 
                 75392763 
                 75398145 
                 protein PBDC1 isoform 2 
               
               
                 PCYT1B 
                 NM_004845 
                 chrX 
                 24576203 
                 24665455 
                 choline-phosphate 
               
               
                   
                   
                   
                   
                   
                 cytidylyltransferase B 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 PCYT1B-AS1 
                 NR_046638 
                 chrX 
                 24668189 
                 24676354 
               
               
                 PDK3 
                 NM_001142386 
                 chrX 
                 24483343 
                 24568583 
                 pyruvate dehydrogenase 
               
               
                   
                   
                   
                   
                   
                 kinase, isozyme 3 isoform 1 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 PDZD11 
                 NM_016484 
                 chrX 
                 69506210 
                 69509798 
                 PDZ domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 11 
               
               
                 PGAM4 
                 NM_001029891 
                 chrX 
                 77223457 
                 77225135 
                 phosphoglycerate mutase 4 
               
               
                 PGRMC1 
                 NM_001282621 
                 chrX 
                 118370207 
                 118378429 
                 membrane-associated 
               
               
                   
                   
                   
                   
                   
                 progesterone receptor 
               
               
                   
                   
                   
                   
                   
                 component 1 isoform 2 
               
               
                 PHEX-AS1 
                 NR_046639 
                 chrX 
                 22180848 
                 22191100 
               
               
                 PHKA1 
                 NM_001172436 
                 chrX 
                 71798663 
                 71934029 
                 phosphorylase b kinase 
               
               
                   
                   
                   
                   
                   
                 regulatory subunit alpha, 
               
               
                   
                   
                   
                   
                   
                 skeletal muscle isoform 
               
               
                   
                   
                   
                   
                   
                 isoform 3 
               
               
                 PHKA2-AS1 
                 NR_029379 
                 chrX 
                 18908413 
                 18913093 
               
               
                 PIH1D3 
                 NM_173494 
                 chrX 
                 106449861 
                 106487473 
                 protein PIH1D3 
               
               
                 PLCXD1 
                 NM_018390 
                 chrY 
                 148060 
                 170022 
                 PI-PLC X domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 1 
               
               
                 PLP1 
                 NM_001128834 
                 chrX 
                 103031438 
                 103047547 
                 myelin proteolipid protein 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 PLS3 
                 NM_001282337 
                 chrX 
                 114795176 
                 114885179 
                 plastin-3 isoform 3 
               
               
                 PLS3-AS1 
                 NR_110383 
                 chrX 
                 114752496 
                 114797058 
               
               
                 PLXNB3 
                 NM_005393 
                 chrX 
                 153029650 
                 153044801 
                 plexin-B3 isoform 1 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 PNCK 
                 NM_001135740 
                 chrX 
                 152935187 
                 152938743 
                 calcium/calmodulin- 
               
               
                   
                   
                   
                   
                   
                 dependent protein kinase 
               
               
                   
                   
                   
                   
                   
                 type 1B isoform b 
               
               
                 PNMA3 
                 NM_013364 
                 chrX 
                 152224765 
                 152228827 
                 paraneoplastic antigen Ma3 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 PPEF1-AS1 
                 NR_046642 
                 chrX 
                 18706762 
                 18710806 
               
               
                 PRKX-AS1 
                 NR_046643 
                 chrX 
                 3577527 
                 3586231 
               
               
                 PRKY 
                 NR_028062 
                 chrY 
                 7142012 
                 7249588 
               
               
                 PRORY 
                 NM_001282471 
                 chrY 
                 23544859 
                 23548246 
                 proline-rich protein, Y- 
               
               
                   
                   
                   
                   
                   
                 linked 
               
               
                 PRPS1 
                 NM_001204402 
                 chrX 
                 106871653 
                 106894256 
                 ribose-phosphate 
               
               
                   
                   
                   
                   
                   
                 pyrophosphokinase 1 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 PRR32 
                 NM_001122716 
                 chrX 
                 125953746 
                 125955768 
                 proline-rich protein 32 
               
               
                 PRRG1 
                 NM_001173489 
                 chrX 
                 37208582 
                 37316548 
                 transmembrane gamma- 
               
               
                   
                   
                   
                   
                   
                 carboxyglutamic acid 
               
               
                   
                   
                   
                   
                   
                 protein 1 isoform 1 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 PRRG3 
                 NM_024082 
                 chrX 
                 150863729 
                 150870063 
                 transmembrane gamma- 
               
               
                   
                   
                   
                   
                   
                 carboxyglutamic acid 
               
               
                   
                   
                   
                   
                   
                 protein 3 precursor 
               
               
                 PRY 
                 NM_004676 
                 chrY 
                 24217902 
                 24242154 
                 PTPN13-like protein, Y- 
               
               
                   
                   
                   
                   
                   
                 linked 
               
               
                 PRY2 
                 NM_001002758 
                 chrY 
                 24217902 
                 24242154 
                 PTPN13-like protein, Y- 
               
               
                   
                   
                   
                   
                   
                 linked 
               
               
                 PSMD10 
                 NM_170750 
                 chrX 
                 107327434 
                 107334874 
                 26S proteasome non-ATPase 
               
               
                   
                   
                   
                   
                   
                 regulatory subunit 10 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 PTCHD1-AS 
                 NR_073010 
                 chrX 
                 22277913 
                 23311263 
               
               
                 RAB40A 
                 NM_080879 
                 chrX 
                 102754680 
                 102774417 
                 ras-related protein Rab-40A 
               
               
                 RAB40AL 
                 NM_001031834 
                 chrX 
                 102192199 
                 102193228 
                 ras-related protein Rab-40A- 
               
               
                   
                   
                   
                   
                   
                 like 
               
               
                 RAB9B 
                 NM_016370 
                 chrX 
                 103077254 
                 103087212 
                 ras-related protein Rab-9B 
               
               
                 RAI2 
                 NM_001172743 
                 chrX 
                 17818168 
                 17879457 
                 retinoic acid-induced protein 
               
               
                   
                   
                   
                   
                   
                 2 isoform 1 
               
               
                 RAP2C 
                 NM_001271187 
                 chrX 
                 131337051 
                 131353508 
                 ras-related protein Rap-2c 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 RAP2C-AS1 
                 NR_110410 
                 chrX 
                 131352534 
                 131566839 
               
               
                 RBMX 
                 NM_002139 
                 chrX 
                 135955605 
                 135962939 
                 RNA-binding motif protein, 
               
               
                   
                   
                   
                   
                   
                 X chromosome isoform 1 
               
               
                 RBMY1A3P 
                 NR_001547 
                 chrY 
                 9154669 
                 9160483 
               
               
                 RBMY2EP 
                 NR_001574 
                 chrY 
                 23557033 
                 23563448 
               
               
                 RENBP 
                 NM_002910 
                 chrX 
                 153200721 
                 153210232 
                 N-acylglucosamine 2- 
               
               
                   
                   
                   
                   
                   
                 epimerase 
               
               
                 REPS2 
                 NM_001080975 
                 chrX 
                 16964813 
                 17171403 
                 ralBP1-associated Eps 
               
               
                   
                   
                   
                   
                   
                 domain-containing protein 2 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 RGAG1 
                 NM_020769 
                 chrX 
                 109662284 
                 109699562 
                 retrotransposon gag domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 1 
               
               
                 RGAG4 
                 NM_001024455 
                 chrX 
                 71346960 
                 71351751 
                 retrotransposon gag domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 4 
               
               
                 RGN 
                 NM_001282848 
                 chrX 
                 46937753 
                 46952713 
                 regucalcin isoform 2 
               
               
                 RIBC1 
                 NM_144968 
                 chrX 
                 53449804 
                 53456776 
                 RIB43A-like with coiled- 
               
               
                   
                   
                   
                   
                   
                 coils protein 1 isoform 2 
               
               
                 RNA45S5 
                 NR_046235 
                 chrUn_gl000220 
                 105423 
                 118780 
               
               
                 RNA5-8S5 
                 NR_003285 
                 chrUn_gl000220 
                 155996 
                 156152 
               
               
                 RNF113A 
                 NM_006978 
                 chrX 
                 119004494 
                 119005791 
                 RING finger protein 113A 
               
               
                 RP11-87M18.2 
                 NR_110412 
                 chrX 
                 36383740 
                 36458375 
               
               
                 RP2 
                 NM_006915 
                 chrX 
                 46696346 
                 46741791 
                 protein XRP2 
               
               
                 RPL36A 
                 NM_001199972 
                 chrX 
                 100645877 
                 100648840 
                 60S ribosomal protein L36a 
               
               
                   
                   
                   
                   
                   
                 isoform b 
               
               
                 RPL36A- 
                 NM_001199973 
                 chrX 
                 100645877 
                 100669128 
                 RPL36A-HNRNPH2 protein 
               
               
                 HNRNPH2 
                   
                   
                   
                   
                 isoform a 
               
               
                 RPL39 
                 NM_001000 
                 chrX 
                 118920466 
                 118925622 
                 60S ribosomal protein L39 
               
               
                 RPS26P11 
                 NR_002309 
                 chrX 
                 71264258 
                 71264811 
               
               
                 RPS4X 
                 NM_001007 
                 chrX 
                 71492452 
                 71497141 
                 40S ribosomal protein S4, X 
               
               
                   
                   
                   
                   
                   
                 isoform X isoform 
               
               
                 RPS4Y1 
                 NM_001008 
                 chrY 
                 2709622 
                 2734997 
                 40S ribosomal protein S4, Y 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 RRAGB 
                 NM_006064 
                 chrX 
                 55744109 
                 55785207 
                 ras-related GTP-binding 
               
               
                   
                   
                   
                   
                   
                 protein B short isoform 
               
               
                 S100G 
                 NM_004057 
                 chrX 
                 16668280 
                 16672791 
                 protein S100-G 
               
               
                 SATL1 
                 NM_001012980 
                 chrX 
                 84347291 
                 84363974 
                 spermidine/spermine N(1)- 
               
               
                   
                   
                   
                   
                   
                 acetyltransferase-like protein 
               
               
                   
                   
                   
                   
                   
                 1 
               
               
                 SCARNA9L 
                 NR_023358 
                 chrX 
                 20154183 
                 20154531 
               
               
                 SCGB1C2 
                 NM_001097610 
                 chr11 
                 193079 
                 194500 
                 secretoglobin family 1C 
               
               
                   
                   
                   
                   
                   
                 member 2 precursor 
               
               
                 SCML1 
                 NM_001037536 
                 chrX 
                 17755568 
                 17773108 
                 sex comb on midleg-like 
               
               
                   
                   
                   
                   
                   
                 protein 1 isoform c 
               
               
                 SEPT6 
                 NM_015129 
                 chrX 
                 118750908 
                 118827333 
                 septin-6 isoform B 
               
               
                 SH2D1A 
                 NM_001114937 
                 chrX 
                 123480131 
                 123507010 
                 SH2 domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 1A isoform 2 
               
               
                 SH3BGRL 
                 NM_003022 
                 chrX 
                 80457302 
                 80554046 
                 SH3 domain-binding 
               
               
                   
                   
                   
                   
                   
                 glutamic acid-rich-like 
               
               
                   
                   
                   
                   
                   
                 protein 
               
               
                 SLC25A5 
                 NM_001152 
                 chrX 
                 118602362 
                 118605359 
                 ADP/ATP translocase 2 
               
               
                 SLC25A5-AS1 
                 NR_028443 
                 chrX 
                 118599995 
                 118603083 
               
               
                 SLC25A53 
                 NM_001012755 
                 chrX 
                 103343897 
                 103401708 
                 solute carrier family 25 
               
               
                   
                   
                   
                   
                   
                 member 53 
               
               
                 SLC9A6 
                 NM_001042537 
                 chrX 
                 135067585 
                 135129428 
                 sodium/hydrogen exchanger 
               
               
                   
                   
                   
                   
                   
                 6 isoform a precursor 
               
               
                 SLITRK2 
                 NM_001144009 
                 chrX 
                 144902865 
                 144907360 
                 SLIT and NTRK-like protein 
               
               
                   
                   
                   
                   
                   
                 2 precursor 
               
               
                 SLITRK4 
                 NM_173078 
                 chrX 
                 142710594 
                 142723019 
                 SLIT and NTRK-like protein 
               
               
                   
                   
                   
                   
                   
                 4 precursor 
               
               
                 SMC1A 
                 NM_006306 
                 chrX 
                 53401069 
                 53449677 
                 structural maintenance of 
               
               
                   
                   
                   
                   
                   
                 chromosomes protein 1A 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 SMIM10 
                 NM_001163438 
                 chrX 
                 134124967 
                 134126503 
                 small integral membrane 
               
               
                   
                   
                   
                   
                   
                 protein 10 
               
               
                 SMIM9 
                 NM_001162936 
                 chrX 
                 154051622 
                 154062937 
                 small integral membrane 
               
               
                   
                   
                   
                   
                   
                 protein 9 precursor 
               
               
                 SMPX 
                 NM_014332 
                 chrX 
                 21724089 
                 21776278 
                 small muscular protein 
               
               
                 SNORA11 
                 NR_002953 
                 chrX 
                 54840802 
                 54840933 
               
               
                 SNORA11C 
                 NR_003710 
                 chrX 
                 47248048 
                 47248175 
               
               
                 SNORA36A 
                 NR_002969 
                 chrX 
                 153996802 
                 153996932 
               
               
                 SNORA56 
                 NR_002984 
                 chrX 
                 154003272 
                 154003401 
               
               
                 SNORA69 
                 NR_002584 
                 chrX 
                 118921315 
                 118921447 
               
               
                 SNORD61 
                 NR_002735 
                 chrX 
                 135961357 
                 135961430 
               
               
                 SOWAHD 
                 NM_001105576 
                 chrX 
                 118892575 
                 118894165 
                 ankyrin repeat domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 
               
               
                   
                   
                   
                   
                   
                 SOWAHD 
               
               
                 SOX3 
                 NM_005634 
                 chrX 
                 139585151 
                 139587225 
                 transcription factor SOX-3 
               
               
                 SPANXN2 
                 NM_001009615 
                 chrX 
                 142795134 
                 142803762 
                 sperm protein associated 
               
               
                   
                   
                   
                   
                   
                 with the nucleus on the X 
               
               
                   
                   
                   
                   
                   
                 chromosome N2 
               
               
                 SPANXN4 
                 NM_001009613 
                 chrX 
                 142113703 
                 142122066 
                 sperm protein associated 
               
               
                   
                   
                   
                   
                   
                 with the nucleus on the X 
               
               
                   
                   
                   
                   
                   
                 chromosome N4 
               
               
                 SPIN3 
                 NM_001010862 
                 chrX 
                 57017263 
                 57021988 
                 spindlin-3 
               
               
                 SPIN4 
                 NM_001012968 
                 chrX 
                 62567106 
                 62571218 
                 spindlin-4 
               
               
                 SPRY3 
                 NM_005840 
                 chrY 
                 59100456 
                 59115123 
                 protein sprouty homolog 3 
               
               
                 SRPK3 
                 NM_001170761 
                 chrX 
                 153046455 
                 153051187 
                 SRSF protein kinase 3 
               
               
                   
                   
                   
                   
                   
                 isoform 3 
               
               
                 SRPX2 
                 NM_014467 
                 chrX 
                 99899162 
                 99926296 
                 sushi repeat-containing 
               
               
                   
                   
                   
                   
                   
                 protein SRPX2 precursor 
               
               
                 SRY 
                 NM_003140 
                 chrY 
                 2654895 
                 2655782 
                 sex-determining region Y 
               
               
                   
                   
                   
                   
                   
                 protein 
               
               
                 SSR4 
                 NM_001204526 
                 chrX 
                 153059903 
                 153063967 
                 translocon-associated protein 
               
               
                   
                   
                   
                   
                   
                 subunit delta isoform 1 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 SSX9 
                 NR_073393 
                 chrX 
                 48160984 
                 48165614 
               
               
                 STK26 
                 NM_016542 
                 chrX 
                 131157244 
                 131209971 
                 serine/threonine-protein 
               
               
                   
                   
                   
                   
                   
                 kinase 26 isoform 1 
               
               
                 SUPT20HL1 
                 NM_001136234 
                 chrX 
                 24380877 
                 24383541 
                 transcription factor SPT20 
               
               
                   
                   
                   
                   
                   
                 homolog-like 1 
               
               
                 SUPT20HL2 
                 NM_001136233 
                 chrX 
                 24328978 
                 24331432 
                 putative transcription factor 
               
               
                   
                   
                   
                   
                   
                 SPT20 homolog-like 2 
               
               
                 SYAP1 
                 NR_033181 
                 chrX 
                 16737706 
                 16780807 
               
               
                 SYN1 
                 NM_133499 
                 chrX 
                 47431299 
                 47479256 
                 synapsin-1 isoform Ib 
               
               
                 SYP-AS1 
                 NR_046649 
                 chrX 
                 49055297 
                 49058913 
               
               
                 TAB3 
                 NM_152787 
                 chrX 
                 30845558 
                 30907511 
                 TGF-beta-activated kinase 1 
               
               
                   
                   
                   
                   
                   
                 and MAP3K7-binding 
               
               
                   
                   
                   
                   
                   
                 protein 3 
               
               
                 TBL1Y 
                 NM_134259 
                 chrY 
                 6778726 
                 6959724 
                 F-box-like/WD repeat- 
               
               
                   
                   
                   
                   
                   
                 containing protein TBL1Y 
               
               
                 TCEAL1 
                 NM_001006640 
                 chrX 
                 102883647 
                 102885876 
                 transcription elongation 
               
               
                   
                   
                   
                   
                   
                 factor A protein-like 1 
               
               
                 TCEAL2 
                 NM_080390 
                 chrX 
                 101380659 
                 101382684 
                 transcription elongation 
               
               
                   
                   
                   
                   
                   
                 factor A protein-like 2 
               
               
                 TCEAL3 
                 NM_001006933 
                 chrX 
                 102862833 
                 102864855 
                 transcription elongation 
               
               
                   
                   
                   
                   
                   
                 factor A protein-like 3 
               
               
                 TCEAL4 
                 NM_001300901 
                 chrX 
                 102831158 
                 102842664 
                 transcription elongation 
               
               
                   
                   
                   
                   
                   
                 factor A protein-like 4 
               
               
                   
                   
                   
                   
                   
                 isoform 5 
               
               
                 TCEAL5 
                 NM_001012979 
                 chrX 
                 102528617 
                 102531797 
                 transcription elongation 
               
               
                   
                   
                   
                   
                   
                 factor A protein-like 5 
               
               
                 TCEAL6 
                 NM_001006938 
                 chrX 
                 101394932 
                 101397388 
                 transcription elongation 
               
               
                   
                   
                   
                   
                   
                 factor A protein-like 6 
               
               
                 TCEAL7 
                 NM_152278 
                 chrX 
                 102585113 
                 102587251 
                 transcription elongation 
               
               
                   
                   
                   
                   
                   
                 factor A protein-like 7 
               
               
                 TCEAL8 
                 NM_001006684 
                 chrX 
                 102507922 
                 102510121 
                 transcription elongation 
               
               
                   
                   
                   
                   
                   
                 factor A protein-like 8 
               
               
                 TCEANC 
                 NM_001297564 
                 chrX 
                 13671224 
                 13683527 
                 transcription elongation 
               
               
                   
                   
                   
                   
                   
                 factor A N-terminal and 
               
               
                   
                   
                   
                   
                   
                 central domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein isoform 2 
               
               
                 TCP11X2 
                 NM_001277423 
                 chrX 
                 101715239 
                 101726732 
                 T-complex protein 11 
               
               
                   
                   
                   
                   
                   
                 homolog 
               
               
                 TDGF1P3 
                 NR_002718 
                 chrX 
                 109763539 
                 109766249 
               
               
                 TENM1 
                 NM_001163279 
                 chrX 
                 123509755 
                 124097666 
                 teneurin-1 isoform 2 
               
               
                 TEX13A 
                 NM_031274 
                 chrX 
                 104463610 
                 104465377 
                 testis-expressed sequence 
               
               
                   
                   
                   
                   
                   
                 13A protein 
               
               
                 TFDP3 
                 NM_016521 
                 chrX 
                 132350696 
                 132352376 
                 transcription factor Dp 
               
               
                   
                   
                   
                   
                   
                 family member 3 
               
               
                 TGIF2LY 
                 NM_139214 
                 chrY 
                 3447125 
                 3448082 
                 homeobox protein TGIF2LY 
               
               
                 THOC2 
                 NM_001081550 
                 chrX 
                 122734411 
                 122866904 
                 THO complex subunit 2 
               
               
                 TIMP1 
                 NM_003254 
                 chrX 
                 47441689 
                 47446190 
                 metalloproteinase inhibitor 1 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 TLR7 
                 NM_016562 
                 chrX 
                 12885201 
                 12908480 
                 toll-like receptor 7 precursor 
               
               
                 TLR8 
                 NM_138636 
                 chrX 
                 12924738 
                 12941288 
                 toll-like receptor 8 isoform 2 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 TLR8-AS1 
                 NR_030727 
                 chrX 
                 12920935 
                 12961419 
               
               
                 TMEM164 
                 NM_017698 
                 chrX 
                 109245862 
                 109421016 
                 transmembrane protein 164 
               
               
                   
                   
                   
                   
                   
                 isoform a precursor 
               
               
                 TMEM255A 
                 NM_017938 
                 chrX 
                 119392504 
                 119445391 
                 transmembrane protein 
               
               
                   
                   
                   
                   
                   
                 255A isoform 1 
               
               
                 TMEM257 
                 NM_004709 
                 chrX 
                 144908927 
                 144911370 
                 transmembrane protein 257 
               
               
                 TMEM27 
                 NM_020665 
                 chrX 
                 15645438 
                 15683154 
                 collectrin precursor 
               
               
                 TMEM31 
                 NM_182541 
                 chrX 
                 102965836 
                 102968960 
                 transmembrane protein 31 
               
               
                 TMLHE-AS1 
                 NR_039991 
                 chrX 
                 154696200 
                 154723771 
               
               
                 TMSB15A 
                 NM_021992 
                 chrX 
                 101768609 
                 101771699 
                 thymosin beta-15A 
               
               
                 TMSB4Y 
                 NM_004202 
                 chrY 
                 15815446 
                 15817902 
                 thymosin beta-4, Y- 
               
               
                   
                   
                   
                   
                   
                 chromosomal 
               
               
                 TNMD 
                 NM_022144 
                 chrX 
                 99839789 
                 99854882 
                 tenomodulin 
               
               
                 TREX2 
                 NM_080701 
                 chrX 
                 152710177 
                 152711945 
                 three prime repair 
               
               
                   
                   
                   
                   
                   
                 exonuclease 2 
               
               
                 TRO 
                 NR_073148 
                 chrX 
                 54946995 
                 54957866 
               
               
                 TRPC5OS 
                 NM_001195578 
                 chrX 
                 111119427 
                 111147213 
                 putative uncharacterized 
               
               
                   
                   
                   
                   
                   
                 protein TRPC5OS 
               
               
                 TSC22D3 
                 NM_004089 
                 chrX 
                 106956451 
                 106960291 
                 TSC22 domain family 
               
               
                   
                   
                   
                   
                   
                 protein 3 isoform 2 
               
               
                 TSIX 
                 NR_003255 
                 chrX 
                 73012039 
                 73049066 
               
               
                 TSPAN6 
                 NM_001278742 
                 chrX 
                 99882104 
                 99892101 
                 tetraspanin-6 isoform c 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 TSPY10 
                 NM_001282469 
                 chrY 
                 9365507 
                 9368122 
                 testis-specific Y-encoded 
               
               
                   
                   
                   
                   
                   
                 protein 10 
               
               
                 TSPYL2 
                 NM_022117 
                 chrX 
                 53111541 
                 53117728 
                 testis-specific Y-encoded- 
               
               
                   
                   
                   
                   
                   
                 like protein 2 
               
               
                 TSR2 
                 NM_058163 
                 chrX 
                 54466852 
                 54471731 
                 pre-rRNA-processing 
               
               
                   
                   
                   
                   
                   
                 protein TSR2 homolog 
               
               
                 TTTY1 
                 NR_001538 
                 chrY 
                 9590764 
                 9611898 
               
               
                 TTTY11 
                 NR_001548 
                 chrY 
                 8651358 
                 8685423 
               
               
                 TTTY12 
                 NR_001551 
                 chrY 
                 7672964 
                 7678723 
               
               
                 TTTY15 
                 NR_001545 
                 chrY 
                 14774297 
                 14804153 
               
               
                 TTTY16 
                 NR_001552 
                 chrY 
                 7567397 
                 7569288 
               
               
                 TTTY18 
                 NR_001550 
                 chrY 
                 8551410 
                 8551919 
               
               
                 TTTY19 
                 NR_001549 
                 chrY 
                 8572512 
                 8573324 
               
               
                 TTTY1B 
                 NR_003589 
                 chrY 
                 9590764 
                 9611928 
               
               
                 TTTY2 
                 NR_001536 
                 chrY 
                 9573894 
                 9596085 
               
               
                 TTTY20 
                 NR_001546 
                 chrY 
                 9167488 
                 9172441 
               
               
                 TTTY21 
                 NR_001535 
                 chrY 
                 9555261 
                 9558905 
               
               
                 TTTY21B 
                 NR_003588 
                 chrY 
                 9555261 
                 9558905 
               
               
                 TTTY22 
                 NR_001539 
                 chrY 
                 9638761 
                 9650854 
               
               
                 TTTY2B 
                 NR_003590 
                 chrY 
                 9573894 
                 9596085 
               
               
                 TTTY3 
                 NR_001524 
                 chrY 
                 27874636 
                 27879535 
               
               
                 TTTY3B 
                 NR_002176 
                 chrY 
                 27874636 
                 27879535 
               
               
                 TTTY6 
                 NR_001527 
                 chrY 
                 24585739 
                 24587606 
               
               
                 TTTY6B 
                 NR_002175 
                 chrY 
                 24585736 
                 24587584 
               
               
                 TTTY7 
                 NR_001534 
                 chrY 
                 9544432 
                 9552871 
               
               
                 TTTY7B 
                 NR_003592 
                 chrY 
                 9544432 
                 9552871 
               
               
                 TTTY8 
                 NR_001533 
                 chrY 
                 9528708 
                 9531308 
               
               
                 TTTY8B 
                 NR_003591 
                 chrY 
                 9528708 
                 9531308 
               
               
                 TTTY9A 
                 NR_001530 
                 chrY 
                 20891767 
                 20901083 
               
               
                 TTTY9B 
                 NR_002159 
                 chrY 
                 20891767 
                 20901083 
               
               
                 TXLNG 
                 NM_018360 
                 chrX 
                 16804554 
                 16862642 
                 gamma-taxilin isoform 1 
               
               
                 TXLNGY 
                 NR_045129 
                 chrY 
                 21729243 
                 21752309 
               
               
                 UBA1 
                 NM_153280 
                 chrX 
                 47050198 
                 47074527 
                 ubiquitin-like modifier- 
               
               
                   
                   
                   
                   
                   
                 activating enzyme 1 
               
               
                 UBE2A 
                 NM_003336 
                 chrX 
                 118708429 
                 118718392 
                 ubiquitin-conjugating 
               
               
                   
                   
                   
                   
                   
                 enzyme E2 A isoform 1 
               
               
                 UBE2DNL 
                 NR_024062 
                 chrX 
                 84189156 
                 84189896 
               
               
                 UBE2E4P 
                 NR_110506 
                 chrX 
                 14262386 
                 14263545 
               
               
                 UPF3B 
                 NM_023010 
                 chrX 
                 118967988 
                 118986991 
                 regulator of nonsense 
               
               
                   
                   
                   
                   
                   
                 transcripts 3B isoform 2 
               
               
                 UQCRBP1 
                 NR_002308 
                 chrX 
                 56763220 
                 56764017 
               
               
                 USP11 
                 NM_004651 
                 chrX 
                 47092313 
                 47107727 
                 ubiquitin carboxyl-terminal 
               
               
                   
                   
                   
                   
                   
                 hydrolase 11 
               
               
                 USP26 
                 NM_031907 
                 chrX 
                 132159506 
                 132162300 
                 ubiquitin carboxyl-terminal 
               
               
                   
                   
                   
                   
                   
                 hydrolase 26 
               
               
                 USP27X 
                 NM_001145073 
                 chrX 
                 49644469 
                 49647168 
                 ubiquitin carboxyl-terminal 
               
               
                   
                   
                   
                   
                   
                 hydrolase 27 
               
               
                 USP27X-AS1 
                 NR_026742 
                 chrX 
                 49641326 
                 49643959 
               
               
                 USP9Y 
                 NM_004654 
                 chrY 
                 14813159 
                 14972768 
                 probable ubiquitin carboxyl- 
               
               
                   
                   
                   
                   
                   
                 terminal hydrolase FAF-Y 
               
               
                 UTY 
                 NR_047602 
                 chrY 
                 15360258 
                 15592550 
               
               
                 UXT 
                 NM_153477 
                 chrX 
                 47511190 
                 47518579 
                 protein UXT isoform 1 
               
               
                 UXT-AS1 
                 NR_028119 
                 chrX 
                 47518231 
                 47519510 
               
               
                 VGLL1 
                 NM_016267 
                 chrX 
                 135614310 
                 135638966 
                 transcription cofactor 
               
               
                   
                   
                   
                   
                   
                 vestigial-like protein 1 
               
               
                 VMA21 
                 NM_001017980 
                 chrX 
                 150565656 
                 150577836 
                 vacuolar ATPase assembly 
               
               
                   
                   
                   
                   
                   
                 integral membrane protein 
               
               
                   
                   
                   
                   
                   
                 VMA21 
               
               
                 VSIG1 
                 NM_182607 
                 chrX 
                 107288199 
                 107322414 
                 V-set and immunoglobulin 
               
               
                   
                   
                   
                   
                   
                 domain-containing protein 1 
               
               
                   
                   
                   
                   
                   
                 isoform 2 precursor 
               
               
                 VSIG4 
                 NM_001184830 
                 chrX 
                 65241579 
                 65259967 
                 V-set and immunoglobulin 
               
               
                   
                   
                   
                   
                   
                 domain-containing protein 4 
               
               
                   
                   
                   
                   
                   
                 isoform 4 precursor 
               
               
                 WBP5 
                 NM_016303 
                 chrX 
                 102611379 
                 102613397 
                 WW domain-binding protein 
               
               
                   
                   
                   
                   
                   
                 5 
               
               
                 WNK3 
                 NM_001002838 
                 chrX 
                 54219255 
                 54384438 
                 serine/threonine-protein 
               
               
                   
                   
                   
                   
                   
                 kinase WNK3 isoform 2 
               
               
                 XAGE2 
                 NM_130777 
                 chrX 
                 52380347 
                 52387021 
                 X antigen family member 2 
               
               
                 XAGE3 
                 NM_130776 
                 chrX 
                 52891557 
                 52896332 
                 X antigen family member 3 
               
               
                 XAGE5 
                 NM_130775 
                 chrX 
                 52841227 
                 52847322 
                 X antigen family member 5 
               
               
                 XGY2 
                 NR_003254 
                 chrY 
                 2620336 
                 2643037 
               
               
                 XIAP 
                 NR_037916 
                 chrX 
                 122994016 
                 123047829 
               
               
                 XIST 
                 NR_001564 
                 chrX 
                 73040485 
                 73072588 
               
               
                 XK 
                 NM_021083 
                 chrX 
                 37545132 
                 37591383 
                 membrane transport protein 
               
               
                   
                   
                   
                   
                   
                 XK precursor 
               
               
                 XKRX 
                 NM_212559 
                 chrX 
                 100168430 
                 100183898 
                 XK-related protein 2 
               
               
                 XKRY 
                 NM_004677 
                 chrY 
                 20297334 
                 20298915 
                 testis-specific XK-related 
               
               
                   
                   
                   
                   
                   
                 protein, Y-linked 2 
               
               
                 XKRY2 
                 NM_001002906 
                 chrY 
                 20297334 
                 20298915 
                 testis-specific XK-related 
               
               
                   
                   
                   
                   
                   
                 protein, Y-linked 2 
               
               
                 XRCC6P5 
                 NR_024608 
                 chrX 
                 98716599 
                 99194841 
               
               
                 YIPF6 
                 NM_173834 
                 chrX 
                 67718623 
                 67757127 
                 protein YIPF6 isoform A 
               
               
                 YY2 
                 NM_206923 
                 chrX 
                 21874104 
                 21876845 
                 transcription factor YY2 
               
               
                 ZBTB33 
                 NM_001184742 
                 chrX 
                 119384609 
                 119392251 
                 transcriptional regulator 
               
               
                   
                   
                   
                   
                   
                 Kaiso 
               
               
                 ZC3H12B 
                 NM_001010888 
                 chrX 
                 64708614 
                 64727767 
                 probable ribonuclease 
               
               
                   
                   
                   
                   
                   
                 ZC3H12B 
               
               
                 ZC4H2 
                 NM_001178033 
                 chrX 
                 64135681 
                 64196413 
                 zinc finger C4H2 domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein isoform 3 
               
               
                 ZCCHC13 
                 NM_203303 
                 chrX 
                 73524024 
                 73524869 
                 zinc finger CCHC domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 13 
               
               
                 ZFP92 
                 NM_001136273 
                 chrX 
                 152683780 
                 152687086 
                 zinc finger protein 92 
               
               
                   
                   
                   
                   
                   
                 homolog 
               
               
                 ZFX-AS1 
                 NR_046657 
                 chrX 
                 24164341 
                 24167771 
               
               
                 ZFY 
                 NM_001145276 
                 chrY 
                 2803111 
                 2850547 
                 zinc finger Y-chromosomal 
               
               
                   
                   
                   
                   
                   
                 protein isoform 3 
               
               
                 ZMAT1 
                 NM_001282400 
                 chrX 
                 101137259 
                 101187039 
                 zinc finger matrin-type 
               
               
                   
                   
                   
                   
                   
                 protein 1 isoform 4 
               
               
                 ZNF157 
                 NM_003446 
                 chrX 
                 47229998 
                 47273098 
                 zinc finger protein 157 
               
               
                 ZNF275 
                 NM_001080485 
                 chrX 
                 152599612 
                 152618384 
                 zinc finger protein 275 
               
               
                 ZNF41 
                 NM_007130 
                 chrX 
                 47305560 
                 47342345 
                 zinc finger protein 41 
               
               
                 ZNF630-AS1 
                 NR_046742 
                 chrX 
                 47915698 
                 47925970 
               
               
                 ZNF674 
                 NM_001146291 
                 chrX 
                 46357159 
                 46404892 
                 zinc finger protein 674 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 ZNF674-AS1 
                 NR_015378 
                 chrX 
                 46404924 
                 46407910 
               
               
                 ZNF711 
                 NM_021998 
                 chrX 
                 84498996 
                 84528368 
                 zinc finger protein 711 
               
               
                 ZNF81 
                 NM_007137 
                 chrX 
                 47696300 
                 47781655 
                 zinc finger protein 81 
               
               
                 ZRSR2 
                 NM_005089 
                 chrX 
                 15808573 
                 15841382 
                 U2 small nuclear 
               
               
                   
                   
                   
                   
                   
                 ribonucleoprotein auxiliary 
               
               
                   
                   
                   
                   
                   
                 factor 35 kDa subunit- 
               
               
                   
                   
                   
                   
                   
                 related protein 2 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 11 
               
             
            
               
                   
               
               
                 The candidate reference loci for use with tissue samples collected 
               
               
                 from healthy subjects, patients with myocardial infarction, and 
               
               
                 cancer-unaffected tissues of cancer patients. 
               
            
           
           
               
               
               
               
               
               
            
               
                 Symbol 
                 Refseq 
                 Chr 
                 Start 
                 End 
                 Description 
               
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 DDX11L16 
                 NR_110561 
                 chrY 
                 59358328 
                 59360854 
                   
               
               
                 LINC00685 
                 NR_027231 
                 chrY 
                 231384 
                 232054 
               
               
                 MIR6089 
                 NR_106737 
                 chrY 
                 2477231 
                 2477295 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 12 
               
             
            
               
                   
               
               
                 The genes, whose CN can be measured using Human Breast Cancer Copy Number 
               
               
                 PCR Array kit (Qiagen) 
               
            
           
           
               
               
               
               
               
               
            
               
                 Symbol 
                 Refseq 
                 Chr 
                 Start 
                 End 
                 Description 
               
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 AKT1 
                 NM_001014431 
                 chr14 
                 105235686 
                 105262080 
                 RAC-alpha 
               
               
                   
                   
                   
                   
                   
                 serine/threonine- 
               
               
                   
                   
                   
                   
                   
                 protein kinase 
               
               
                 AURKA 
                 NM_198437 
                 chr20 
                 54944444 
                 54967351 
                 aurora kinase A 
               
               
                 BCHE 
                 NM_000055 
                 chr3 
                 165490691 
                 165555253 
                 cholinesterase 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 BCL2L1 
                 NM_001191 
                 chr20 
                 30252260 
                 30310656 
                 bcl-2-like protein 1 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 C11orf30 
                 NM_001300944 
                 chr11 
                 76156068 
                 76263943 
                 protein EMSY 
               
               
                   
                   
                   
                   
                   
                 isoform 3 
               
               
                 CCND1 
                 NM_053056 
                 chr11 
                 69455872 
                 69469242 
                 G1/S-specific 
               
               
                   
                   
                   
                   
                   
                 cyclin-D1 
               
               
                 CDK4 
                 NM_000075 
                 chr12 
                 58141509 
                 58146230 
                 cyclin-dependent 
               
               
                   
                   
                   
                   
                   
                 kinase 4 
               
               
                 CDKN2A 
                 NM_058197 
                 chr9 
                 21967750 
                 21974826 
                 cyclin-dependent 
               
               
                   
                   
                   
                   
                   
                 kinase inhibitor 2A 
               
               
                   
                   
                   
                   
                   
                 isoform p12 
               
               
                 CSMD1 
                 NM_033225 
                 chr8 
                 2792874 
                 4852328 
                 CUB and sushi 
               
               
                   
                   
                   
                   
                   
                 domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 1 precursor 
               
               
                 EGFR 
                 NM_201283 
                 chr7 
                 55086724 
                 55224644 
                 epidermal growth 
               
               
                   
                   
                   
                   
                   
                 factor receptor 
               
               
                   
                   
                   
                   
                   
                 isoform c precursor 
               
               
                 ERBB2 
                 NM_004448 
                 chr17 
                 37856230 
                 37884915 
                 receptor tyrosine- 
               
               
                   
                   
                   
                   
                   
                 protein kinase erbB- 
               
               
                   
                   
                   
                   
                   
                 2 isoform a 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 FGFR1 
                 NM_023106 
                 chr8 
                 38268655 
                 38326352 
                 fibroblast growth 
               
               
                   
                   
                   
                   
                   
                 factor receptor 1 
               
               
                   
                   
                   
                   
                   
                 isoform 4 precursor 
               
               
                 FGFR2 
                 NM_001144919 
                 chr10 
                 123241366 
                 123357972 
                 fibroblast growth 
               
               
                   
                   
                   
                   
                   
                 factor receptor 2 
               
               
                   
                   
                   
                   
                   
                 isoform 9 precursor 
               
               
                 MTDH 
                 NM_178812 
                 chr8 
                 98656406 
                 98742488 
                 protein LYRIC 
               
               
                 MYC 
                 NM_002467 
                 chr8 
                 128748314 
                 128753680 
                 myc proto- 
               
               
                   
                   
                   
                   
                   
                 oncogene protein 
               
               
                 NCOA3 
                 NM_001174088 
                 chr20 
                 46130600 
                 46285621 
                 nuclear receptor 
               
               
                   
                   
                   
                   
                   
                 coactivator 3 
               
               
                   
                   
                   
                   
                   
                 isoform d 
               
               
                 PAK1 
                 NM_002576 
                 chr11 
                 77033059 
                 77185108 
                 serine/threonine- 
               
               
                   
                   
                   
                   
                   
                 protein kinase PAK 
               
               
                   
                   
                   
                   
                   
                 1 isoform 2 
               
               
                 PPAPDC1B 
                 NM_001102560 
                 chr8 
                 38124497 
                 38126738 
                 phosphatidate 
               
               
                   
                   
                   
                   
                   
                 phosphatase 
               
               
                   
                   
                   
                   
                   
                 PPAPDC1B 
               
               
                   
                   
                   
                   
                   
                 isoform 3 
               
               
                 PTEN 
                 NM_000314 
                 chr10 
                 89623194 
                 89728532 
                 phosphatidylinositol 
               
               
                   
                   
                   
                   
                   
                 3,4,5-trisphosphate 
               
               
                   
                   
                   
                   
                   
                 3-phosphatase and 
               
               
                   
                   
                   
                   
                   
                 dual-specificity 
               
               
                   
                   
                   
                   
                   
                 protein phosphatase 
               
               
                   
                   
                   
                   
                   
                 PTEN 
               
               
                 PTK2 
                 NM_001199649 
                 chr8 
                 141668480 
                 142011412 
                 focal adhesion 
               
               
                   
                   
                   
                   
                   
                 kinase 1 isoform c 
               
               
                 RB1 
                 NM_000321 
                 chr13 
                 48877882 
                 49056026 
                 retinoblastoma- 
               
               
                   
                   
                   
                   
                   
                 associated protein 
               
               
                 TFDP1 
                 NR_026580 
                 chr13 
                 114239002 
                 114295788 
               
               
                 TOP2A 
                 NM_001067 
                 chr17 
                 38544772 
                 38574202 
                 DNA 
               
               
                   
                   
                   
                   
                   
                 topoisomerase 2- 
               
               
                   
                   
                   
                   
                   
                 alpha 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 13 
               
             
            
               
                   
               
               
                 Genes with high expression and CN-invariant in the TCGA EOC samples. 
               
            
           
           
               
               
               
               
               
               
            
               
                 Symbol 
                 Refseq 
                 Chr 
                 Start 
                 End 
                 Description 
               
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 ABCB4 
                 NM_018849 
                 chr7 
                 87031360 
                 87105019 
                 multidrug resistance 
               
               
                   
                   
                   
                   
                   
                 protein 3 isoform B 
               
               
                 ABHD5 
                 NM_016006 
                 chr3 
                 43732374 
                 43764217 
                 1-acylglycerol-3- 
               
               
                   
                   
                   
                   
                   
                 phosphate O- 
               
               
                   
                   
                   
                   
                   
                 acyltransferase ABHD5 
               
               
                 ACYP2 
                 NM_138448 
                 chr2 
                 54342409 
                 54532435 
                 acylphosphatase-2 
               
               
                 AFF3 
                 NM_001025108 
                 chr2 
                 100163715 
                 100722045 
                 AF4/FMR2 family 
               
               
                   
                   
                   
                   
                   
                 member 3 isoform 2 
               
               
                 AGAP1 
                 NM_001244888 
                 chr2 
                 236402732 
                 236761846 
                 arf-GAP with GTPase, 
               
               
                   
                   
                   
                   
                   
                 ANK repeat and PH 
               
               
                   
                   
                   
                   
                   
                 domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 1 isoform 3 
               
               
                 AMD1 
                 NM_001287216 
                 chr6 
                 111195986 
                 111216915 
                 S-adenosylmethionine 
               
               
                   
                   
                   
                   
                   
                 decarboxylase 
               
               
                   
                   
                   
                   
                   
                 proenzyme isoform 5 
               
               
                 ANK2 
                 NM_001127493 
                 chr4 
                 113739238 
                 114304896 
                 ankyrin-2 isoform 3 
               
               
                 ARSE 
                 NM_001282628 
                 chrX 
                 2852672 
                 2882494 
                 arylsulfatase E isoform 1 
               
               
                 ASAP1 
                 NM_018482 
                 chr8 
                 131064350 
                 131455906 
                 arf-GAP with SH3 
               
               
                   
                   
                   
                   
                   
                 domain, ANK repeat 
               
               
                   
                   
                   
                   
                   
                 and PH domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 1 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 ASCC3 
                 NM_001284271 
                 chr6 
                 101163006 
                 101329248 
                 activating signal 
               
               
                   
                   
                   
                   
                   
                 cointegrator 1 complex 
               
               
                   
                   
                   
                   
                   
                 subunit 3 isoform c 
               
               
                 ATAD2B 
                 NM_001242338 
                 chr2 
                 23971533 
                 24149984 
                 ATPase family AAA 
               
               
                   
                   
                   
                   
                   
                 domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 2B isoform 2 
               
               
                 ATF7IP2 
                 NM_024997 
                 chr16 
                 10479911 
                 10577495 
                 activating transcription 
               
               
                   
                   
                   
                   
                   
                 factor 7-interacting 
               
               
                   
                   
                   
                   
                   
                 protein 2 isoform 1 
               
               
                 ATXN7 
                 NM_001128149 
                 chr3 
                 63953419 
                 63989136 
                 ataxin-7 isoform c 
               
               
                 AUTS2 
                 NM_015570 
                 chr7 
                 69063904 
                 70258054 
                 autism susceptibility 
               
               
                   
                   
                   
                   
                   
                 gene 2 protein isoform 1 
               
               
                 BATF3 
                 NM_018664 
                 chr1 
                 212859758 
                 212873327 
                 basic leucine zipper 
               
               
                   
                   
                   
                   
                   
                 transcriptional factor 
               
               
                   
                   
                   
                   
                   
                 ATF-like 3 
               
               
                 BMPR2 
                 NM_001204 
                 chr2 
                 203241049 
                 203432474 
                 bone morphogenetic 
               
               
                   
                   
                   
                   
                   
                 protein receptor type-2 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 BTNL8 
                 NM_001159707 
                 chr5 
                 180326076 
                 180377906 
                 butyrophilin-like protein 
               
               
                   
                   
                   
                   
                   
                 8 isoform 3 precursor 
               
               
                 C1orf21 
                 NM_030806 
                 chr1 
                 184356149 
                 184598155 
                 uncharacterized protein 
               
               
                   
                   
                   
                   
                   
                 C1orf21 
               
               
                 CACNB2 
                 NM_201571 
                 chr10 
                 18429741 
                 18830688 
                 voltage-dependent L- 
               
               
                   
                   
                   
                   
                   
                 type calcium channel 
               
               
                   
                   
                   
                   
                   
                 subunit beta-2 isoform 6 
               
               
                 CAMTA1 
                 NR_038934 
                 chr1 
                 6845383 
                 6948261 
               
               
                 CASC5 
                 NM_170589 
                 chr15 
                 40886446 
                 40954881 
                 protein CASC5 isoform 1 
               
               
                 CASQ2 
                 NM_001232 
                 chr1 
                 116242625 
                 116311426 
                 calsequestrin-2 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 CCDC88A 
                 NM_018084 
                 chr2 
                 55514977 
                 55647057 
                 girdin isoform 2 
               
               
                 CHL1 
                 NR_045572 
                 chr3 
                 239325 
                 290282 
               
               
                 CHST15 
                 NM_014863 
                 chr10 
                 125779168 
                 125851940 
                 carbohydrate 
               
               
                   
                   
                   
                   
                   
                 sulfotransferase 15 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 CLASP1 
                 NM_001142273 
                 chr2 
                 122095351 
                 122407052 
                 CLIP-associating 
               
               
                   
                   
                   
                   
                   
                 protein 1 isoform 2 
               
               
                 CLIC4 
                 NM_013943 
                 chr1 
                 25071759 
                 25170815 
                 chloride intracellular 
               
               
                   
                   
                   
                   
                   
                 channel protein 4 
               
               
                 CLMN 
                 NM_024734 
                 chr14 
                 95648275 
                 95786245 
                 calmin 
               
               
                 COPA 
                 NM_001098398 
                 chr1 
                 160258376 
                 160313354 
                 coatomer subunit alpha 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 CUL3 
                 NM_001257197 
                 chr2 
                 225334866 
                 225450114 
                 cullin-3 isoform 2 
               
               
                 DAB1 
                 NM_021080 
                 chr1 
                 57463578 
                 58716211 
                 disabled homolog 1 
               
               
                 DAPK1 
                 NM_001288729 
                 chr9 
                 90113449 
                 90323549 
                 death-associated protein 
               
               
                   
                   
                   
                   
                   
                 kinase 1 
               
               
                 DDAH1 
                 NM_012137 
                 chr1 
                 85784167 
                 85930889 
                 N(G),N(G)- 
               
               
                   
                   
                   
                   
                   
                 dimethylarginine 
               
               
                   
                   
                   
                   
                   
                 dimethylaminohydrolase 
               
               
                   
                   
                   
                   
                   
                 1 isoform 1 
               
               
                 DEGS1 
                 NM_003676 
                 chr1 
                 224370909 
                 224381142 
                 sphingolipid delta(4)- 
               
               
                   
                   
                   
                   
                   
                 desaturase DES1 
               
               
                 DEPDC1 
                 NM_001114120 
                 chr1 
                 68939834 
                 68962904 
                 DEP domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 1A isoform a 
               
               
                 DNM3 
                 NM_015569 
                 chr1 
                 171810617 
                 172381857 
                 dynamin-3 isoform a 
               
               
                 DPPA4 
                 NM_018189 
                 chr3 
                 109044987 
                 109056419 
                 developmental 
               
               
                   
                   
                   
                   
                   
                 pluripotency-associated 
               
               
                   
                   
                   
                   
                   
                 protein 4 
               
               
                 DYRK1A 
                 NM_001396 
                 chr21 
                 38792601 
                 38887679 
                 dual specificity tyrosine- 
               
               
                   
                   
                   
                   
                   
                 phosphorylation- 
               
               
                   
                   
                   
                   
                   
                 regulated kinase 1A 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 EFHC2 
                 NM_025184 
                 chrX 
                 44007127 
                 44202923 
                 EF-hand domain- 
               
               
                   
                   
                   
                   
                   
                 containing family 
               
               
                   
                   
                   
                   
                   
                 member C2 
               
               
                 EHBP1 
                 NM_015252 
                 chr2 
                 62933000 
                 63273621 
                 EH domain-binding 
               
               
                   
                   
                   
                   
                   
                 protein 1 isoform 1 
               
               
                 EHD3 
                 NM_014600 
                 chr2 
                 31456879 
                 31491260 
                 EH domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 3 
               
               
                 EIF5 
                 NM_001969 
                 chr14 
                 103800338 
                 103811361 
                 eukaryotic translation 
               
               
                   
                   
                   
                   
                   
                 initiation factor 5 
               
               
                 ENPP2 
                 NR_045555 
                 chr8 
                 120569316 
                 120605248 
               
               
                 EPB41 
                 NM_001166007 
                 chr1 
                 29213602 
                 29446558 
                 protein 4.1 isoform 5 
               
               
                 EPHB2 
                 NM_004442 
                 chr1 
                 23037330 
                 23241823 
                 ephrin type-B receptor 2 
               
               
                   
                   
                   
                   
                   
                 isoform 2 precursor 
               
               
                 ERBB4 
                 NM_005235 
                 chr2 
                 212240441 
                 213403352 
                 receptor tyrosine-protein 
               
               
                   
                   
                   
                   
                   
                 kinase erbB-4 isoform 
               
               
                   
                   
                   
                   
                   
                 JM-a/CVT-1 precursor 
               
               
                 ERC2 
                 NM_015576 
                 chr3 
                 55542335 
                 56502391 
                 ERC protein 2 
               
               
                 ESRRG 
                 NM_206594 
                 chr1 
                 216676587 
                 217262987 
                 estrogen-related 
               
               
                   
                   
                   
                   
                   
                 receptor gamma isoform 2 
               
               
                 FAHD2A 
                 NM_016044 
                 chr2 
                 96068447 
                 96078879 
                 fumarylacetoacetate 
               
               
                   
                   
                   
                   
                   
                 hydrolase domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 2A 
               
               
                 FAM49A 
                 NM_030797 
                 chr2 
                 16730729 
                 16847134 
                 protein FAM49A 
               
               
                 FAT1 
                 NM_005245 
                 chr4 
                 187508936 
                 187644987 
                 protocadherin Fat 1 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 FCGR2A 
                 NM_001136219 
                 chr1 
                 161475204 
                 161489360 
                 low affinity 
               
               
                   
                   
                   
                   
                   
                 immunoglobulin gamma 
               
               
                   
                   
                   
                   
                   
                 Fc region receptor II-a 
               
               
                   
                   
                   
                   
                   
                 isoform 1 precursor 
               
               
                 FGF12 
                 NM_004113 
                 chr3 
                 191857181 
                 192445388 
                 fibroblast growth factor 
               
               
                   
                   
                   
                   
                   
                 12 isoform 2 
               
               
                 FGGY 
                 NM_001113411 
                 chr1 
                 59762624 
                 60228402 
                 FGGY carbohydrate 
               
               
                   
                   
                   
                   
                   
                 kinase domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 
               
               
                   
                   
                   
                   
                   
                 isoform a 
               
               
                 FHIT 
                 NM_002012 
                 chr3 
                 59735035 
                 61237133 
                 bis(5′-adenosyl)- 
               
               
                   
                   
                   
                   
                   
                 triphosphatase 
               
               
                 FHL1 
                 NM_001159702 
                 chrX 
                 135229558 
                 135293518 
                 four and a half LIM 
               
               
                   
                   
                   
                   
                   
                 domains protein 1 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 FHL2 
                 NM_201557 
                 chr2 
                 105977282 
                 106055230 
                 four and a half LIM 
               
               
                   
                   
                   
                   
                   
                 domains protein 2 
               
               
                 FUT9 
                 NM_006581 
                 chr6 
                 96463844 
                 96663488 
                 alpha-(1,3)- 
               
               
                   
                   
                   
                   
                   
                 fucosyltransferase 9 
               
               
                 GAP43 
                 NM_002045 
                 chr3 
                 115342150 
                 115440334 
                 neuromodulin isoform 2 
               
               
                 GBE1 
                 NM_000158 
                 chr3 
                 81538849 
                 81810950 
                 1,4-alpha-glucan- 
               
               
                   
                   
                   
                   
                   
                 branching enzyme 
               
               
                 GLI2 
                 NM_005270 
                 chr2 
                 121554866 
                 121750229 
                 zinc finger protein GLI2 
               
               
                 GOLIM4 
                 NM_014498 
                 chr3 
                 167727653 
                 167813417 
                 Golgi integral 
               
               
                   
                   
                   
                   
                   
                 membrane protein 4 
               
               
                 GPBP1L1 
                 NM_021639 
                 chr1 
                 46092975 
                 46152302 
                 vasculin-like protein 1 
               
               
                 GRM8 
                 NM_001127323 
                 chr7 
                 126078651 
                 126892428 
                 metabotropic glutamate 
               
               
                   
                   
                   
                   
                   
                 receptor 8 isoform b 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 GTF2F2 
                 NM_004128 
                 chr13 
                 45694630 
                 45858239 
                 general transcription 
               
               
                   
                   
                   
                   
                   
                 factor IIF subunit 2 
               
               
                 H6PD 
                 NM_001282587 
                 chr1 
                 9299902 
                 9331394 
                 GDH/6PGL 
               
               
                   
                   
                   
                   
                   
                 endoplasmic 
               
               
                   
                   
                   
                   
                   
                 bifunctional protein 
               
               
                   
                   
                   
                   
                   
                 isoform 1 precursor 
               
               
                 HHAT 
                 NM_001122834 
                 chr1 
                 210501595 
                 210849638 
                 protein-cysteine N- 
               
               
                   
                   
                   
                   
                   
                 palmitoyltransferase 
               
               
                   
                   
                   
                   
                   
                 HHAT isoform 1 
               
               
                 HS3ST1 
                 NM_005114 
                 chr4 
                 11399987 
                 11430537 
                 heparan sulfate 
               
               
                   
                   
                   
                   
                   
                 glucosamine 3-O- 
               
               
                   
                   
                   
                   
                   
                 sulfotransferase 1 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 HTR4 
                 NM_199453 
                 chr5 
                 147830594 
                 148016624 
                 5-hydroxytryptamine 
               
               
                   
                   
                   
                   
                   
                 receptor 4 isoform g 
               
               
                 HYAL3 
                 NM_003549 
                 chr3 
                 50330258 
                 50336899 
                 hyaluronidase-3 isoform 
               
               
                   
                   
                   
                   
                   
                 1 precursor 
               
               
                 IL15 
                 NR_037840 
                 chr4 
                 142557748 
                 142655140 
               
               
                 IL5RA 
                 NM_175726 
                 chr3 
                 3108007 
                 3152058 
                 interleukin-5 receptor 
               
               
                   
                   
                   
                   
                   
                 subunit alpha isoform 1 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 KCNAB1 
                 NM_172159 
                 chr3 
                 156008775 
                 156256927 
                 voltage-gated potassium 
               
               
                   
                   
                   
                   
                   
                 channel subunit beta-1 
               
               
                   
                   
                   
                   
                   
                 isoform 3 
               
               
                 LAMC3 
                 NM_006059 
                 chr9 
                 133884503 
                 133968446 
                 laminin subunit gamma- 
               
               
                   
                   
                   
                   
                   
                 3 precursor 
               
               
                 LDB2 
                 NM_001290 
                 chr4 
                 16503164 
                 16900424 
                 LIM domain-binding 
               
               
                   
                   
                   
                   
                   
                 protein 2 isoform a 
               
               
                 LEF1 
                 NM_001130714 
                 chr4 
                 108968700 
                 109090112 
                 lymphoid enhancer- 
               
               
                   
                   
                   
                   
                   
                 binding factor 1 isoform 3 
               
               
                 LPHN3 
                 NM_015236 
                 chr4 
                 62362838 
                 62938168 
                 latrophilin-3 precursor 
               
               
                 LRCH1 
                 NM_015116 
                 chr13 
                 47127295 
                 47319036 
                 leucine-rich repeat and 
               
               
                   
                   
                   
                   
                   
                 calponin homology 
               
               
                   
                   
                   
                   
                   
                 domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 1 isoform 2 
               
               
                 LRP1B 
                 NM_018557 
                 chr2 
                 140988995 
                 142889270 
                 low-density lipoprotein 
               
               
                   
                   
                   
                   
                   
                 receptor-related protein 
               
               
                   
                   
                   
                   
                   
                 1B precursor 
               
               
                 LYST 
                 NM_001301365 
                 chr1 
                 235824330 
                 236047008 
                 lysosomal-trafficking 
               
               
                   
                   
                   
                   
                   
                 regulator 
               
               
                 MAN1A1 
                 NM_005907 
                 chr6 
                 119498365 
                 119670931 
                 mannosyl- 
               
               
                   
                   
                   
                   
                   
                 oligosaccharide 1,2- 
               
               
                   
                   
                   
                   
                   
                 alpha-mannosidase IA 
               
               
                 MCTP1 
                 NM_001002796 
                 chr5 
                 94041241 
                 94417570 
                 multiple C2 and 
               
               
                   
                   
                   
                   
                   
                 transmembrane domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 1 
               
               
                   
                   
                   
                   
                   
                 isoform S 
               
               
                 MFAP3L 
                 NM_021647 
                 chr4 
                 170907747 
                 170947581 
                 microfibrillar-associated 
               
               
                   
                   
                   
                   
                   
                 protein 3-like isoform 1 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 MORC3 
                 NM_015358 
                 chr21 
                 37692486 
                 37748944 
                 MORC family CW-type 
               
               
                   
                   
                   
                   
                   
                 zinc finger protein 3 
               
               
                 MTA1 
                 NM_001203258 
                 chr14 
                 105886185 
                 105937057 
                 metastasis-associated 
               
               
                   
                   
                   
                   
                   
                 protein MTA1 isoform 
               
               
                   
                   
                   
                   
                   
                 MTA1s 
               
               
                 NECAP2 
                 NM_001145278 
                 chr1 
                 16767166 
                 16786584 
                 adaptin ear-binding 
               
               
                   
                   
                   
                   
                   
                 coat-associated protein 2 
               
               
                   
                   
                   
                   
                   
                 isoform 3 
               
               
                 NEIL3 
                 NM_018248 
                 chr4 
                 178230990 
                 178284092 
                 endonuclease 8-like 3 
               
               
                 NLGN4X 
                 NM_181332 
                 chrX 
                 5808066 
                 6146923 
                 neuroligin-4, X-linked 
               
               
                 NMD3 
                 NM_015938 
                 chr3 
                 160939098 
                 160969795 
                 60S ribosomal export 
               
               
                   
                   
                   
                   
                   
                 protein NMD3 
               
               
                 NOTCH2 
                 NM_024408 
                 chr1 
                 120454175 
                 120612317 
                 neurogenic locus notch 
               
               
                   
                   
                   
                   
                   
                 homolog protein 2 
               
               
                   
                   
                   
                   
                   
                 isoform 1 preproprotein 
               
               
                 NRP2 
                 NM_018534 
                 chr2 
                 206547223 
                 206641880 
                 neuropilin-2 isoform 4 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 NRXN1 
                 NM_004801 
                 chr2 
                 50145642 
                 51259674 
                 neurexin-1-beta isoform 
               
               
                   
                   
                   
                   
                   
                 alpha1 precursor 
               
               
                 NT5C2 
                 NM_001134373 
                 chr10 
                 104847773 
                 104953063 
                 cytosolic purine 5′- 
               
               
                   
                   
                   
                   
                   
                 nucleotidase 
               
               
                 NTNG1 
                 NM_014917 
                 chr1 
                 107682744 
                 108024475 
                 netrin-G1 isoform 3 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 NUP133 
                 NM_018230 
                 chr1 
                 229577043 
                 229644088 
                 nuclear pore complex 
               
               
                   
                   
                   
                   
                   
                 protein Nup133 
               
               
                 PARN 
                 NM_001134477 
                 chr16 
                 14529556 
                 14724128 
                 poly(A)-specific 
               
               
                   
                   
                   
                   
                   
                 ribonuclease PARN 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 PCDH7 
                 NM_032456 
                 chr4 
                 30722029 
                 30726957 
                 protocadherin-7 isoform 
               
               
                   
                   
                   
                   
                   
                 b precursor 
               
               
                 PCOLCE2 
                 NM_013363 
                 chr3 
                 142536701 
                 142608045 
                 procollagen C- 
               
               
                   
                   
                   
                   
                   
                 endopeptidase enhancer 
               
               
                   
                   
                   
                   
                   
                 2 precursor 
               
               
                 PDE2A 
                 NM_001146209 
                 chr11 
                 72287183 
                 72380108 
                 cGMP-dependent 3′,5′- 
               
               
                   
                   
                   
                   
                   
                 cyclic 
               
               
                   
                   
                   
                   
                   
                 phosphodiesterase 
               
               
                   
                   
                   
                   
                   
                 isoform PDE2A4 
               
               
                 PDE6C 
                 NM_006204 
                 chr10 
                 95372344 
                 95425429 
                 cone cGMP-specific 
               
               
                   
                   
                   
                   
                   
                 3′,5′-cyclic 
               
               
                   
                   
                   
                   
                   
                 phosphodiesterase 
               
               
                   
                   
                   
                   
                   
                 subunit alpha′ 
               
               
                 PDIA3 
                 NM_005313 
                 chr15 
                 44038589 
                 44064804 
                 protein disulfide- 
               
               
                   
                   
                   
                   
                   
                 isomerase A3 precursor 
               
               
                 PDZK1 
                 NM_001201325 
                 chr1 
                 145727665 
                 145764206 
                 Na(+)/H(+) exchange 
               
               
                   
                   
                   
                   
                   
                 regulatory cofactor 
               
               
                   
                   
                   
                   
                   
                 NHE-RF3 isoform 1 
               
               
                 PHTF1 
                 NM_006608 
                 chr1 
                 114239823 
                 114301777 
                 putative homeodomain 
               
               
                   
                   
                   
                   
                   
                 transcription factor 1 
               
               
                 PLEKHA2 
                 NM_021623 
                 chr8 
                 38758752 
                 38831430 
                 pleckstrin homology 
               
               
                   
                   
                   
                   
                   
                 domain-containing 
               
               
                   
                   
                   
                   
                   
                 family A member 2 
               
               
                 POU2F1 
                 NM_001198783 
                 chr1 
                 167298280 
                 167396582 
                 POU domain, class 2, 
               
               
                   
                   
                   
                   
                   
                 transcription factor 1 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 PRDM16 
                 NM_022114 
                 chr1 
                 2985741 
                 3355185 
                 PR domain zinc finger 
               
               
                   
                   
                   
                   
                   
                 protein 16 isoform 1 
               
               
                 PRDM5 
                 NM_001300824 
                 chr4 
                 121613067 
                 121844021 
                 PR domain zinc finger 
               
               
                   
                   
                   
                   
                   
                 protein 5 isfoorm 3 
               
               
                 PRKCE 
                 NM_005400 
                 chr2 
                 45879042 
                 46415129 
                 protein kinase C epsilon 
               
               
                   
                   
                   
                   
                   
                 type 
               
               
                 PRKCZ 
                 NM_001033582 
                 chr1 
                 2036154 
                 2116834 
                 protein kinase C zeta 
               
               
                   
                   
                   
                   
                   
                 type isoform 2 
               
               
                 PRUNE 
                 NM_021222 
                 chr1 
                 150980972 
                 151008189 
                 protein prune homolog 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 PTGS2 
                 NM_000963 
                 chr1 
                 186640943 
                 186649559 
                 prostaglandin G/H 
               
               
                   
                   
                   
                   
                   
                 synthase 2 precursor 
               
               
                 PTPRF 
                 NM_130440 
                 chr1 
                 43996546 
                 44089343 
                 receptor-type tyrosine- 
               
               
                   
                   
                   
                   
                   
                 protein phosphatase F 
               
               
                   
                   
                   
                   
                   
                 isoform 2 precursor 
               
               
                 PTPRZ1 
                 NM_002851 
                 chr7 
                 121513158 
                 121702090 
                 receptor-type tyrosine- 
               
               
                   
                   
                   
                   
                   
                 protein phosphatase zeta 
               
               
                   
                   
                   
                   
                   
                 isoform 1 precursor 
               
               
                 PUM1 
                 NM_014676 
                 chr1 
                 31404352 
                 31538564 
                 pumilio homolog 1 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 RAD52 
                 NM_001297419 
                 chr12 
                 1020901 
                 1099207 
                 DNA repair protein 
               
               
                   
                   
                   
                   
                   
                 RAD52 homolog 
               
               
                   
                   
                   
                   
                   
                 isoform a 
               
               
                 RAI2 
                 NM_001172743 
                 chrX 
                 17818168 
                 17879457 
                 retinoic acid-induced 
               
               
                   
                   
                   
                   
                   
                 protein 2 isoform 1 
               
               
                 RNF144A 
                 NM_014746 
                 chr2 
                 7057522 
                 7184309 
                 E3 ubiquitin-protein 
               
               
                   
                   
                   
                   
                   
                 ligase RNF144A 
               
               
                 SCHIP1 
                 NM_014575 
                 chr3 
                 158991035 
                 159615155 
                 schwannomin- 
               
               
                   
                   
                   
                   
                   
                 interacting protein 1 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 SERTAD2 
                 NM_014755 
                 chr2 
                 64858754 
                 64881046 
                 SERTA domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 2 
               
               
                 SLC12A6 
                 NM_001042495 
                 chr15 
                 34522196 
                 34630265 
                 solute carrier family 12 
               
               
                   
                   
                   
                   
                   
                 member 6 isoform c 
               
               
                 SLC15A2 
                 NM_001145998 
                 chr3 
                 121613170 
                 121663034 
                 solute carrier family 15 
               
               
                   
                   
                   
                   
                   
                 member 2 isoform b 
               
               
                 SLC4A4 
                 NM_003759 
                 chr4 
                 72204769 
                 72437804 
                 electrogenic sodium 
               
               
                   
                   
                   
                   
                   
                 bicarbonate 
               
               
                   
                   
                   
                   
                   
                 cotransporter 1 isoform 2 
               
               
                 SMYD3 
                 NM_022743 
                 chr1 
                 245912641 
                 246580714 
                 histone-lysine N- 
               
               
                   
                   
                   
                   
                   
                 methyltransferase 
               
               
                   
                   
                   
                   
                   
                 SMYD3 isoform 2 
               
               
                 SNTG2 
                 NM_018968 
                 chr2 
                 946553 
                 1371384 
                 gamma-2-syntrophin 
               
               
                 SPATS2L 
                 NM_001100424 
                 chr2 
                 201170984 
                 201346986 
                 SPATS2-like protein 
               
               
                   
                   
                   
                   
                   
                 isoform b 
               
               
                 TBL1X 
                 NM_001139468 
                 chrX 
                 9431334 
                 9687780 
                 F-box-like/WD repeat- 
               
               
                   
                   
                   
                   
                   
                 containing protein 
               
               
                   
                   
                   
                   
                   
                 TBL1X isoform b 
               
               
                 TGFBR3 
                 NM_001195683 
                 chr1 
                 92145899 
                 92351836 
                 transforming growth 
               
               
                   
                   
                   
                   
                   
                 factor beta receptor type 
               
               
                   
                   
                   
                   
                   
                 3 isoform b precursor 
               
               
                 THRAP3 
                 NM_005119 
                 chr1 
                 36690016 
                 36770957 
                 thyroid hormone 
               
               
                   
                   
                   
                   
                   
                 receptor-associated 
               
               
                   
                   
                   
                   
                   
                 protein 3 
               
               
                 TIAM1 
                 NM_003253 
                 chr21 
                 32490735 
                 32931290 
                 T-lymphoma invasion 
               
               
                   
                   
                   
                   
                   
                 and metastasis-inducing 
               
               
                   
                   
                   
                   
                   
                 protein 1 
               
               
                 TLE4 
                 NM_007005 
                 chr9 
                 82186687 
                 82341796 
                 transducin-like enhancer 
               
               
                   
                   
                   
                   
                   
                 protein 4 isoform 3 
               
               
                 TNIK 
                 NM_001161561 
                 chr3 
                 170780291 
                 171178197 
                 TRAF2 and NCK- 
               
               
                   
                   
                   
                   
                   
                 interacting protein 
               
               
                   
                   
                   
                   
                   
                 kinase isoform 3 
               
               
                 TRIM48 
                 NM_024114 
                 chr11 
                 55029657 
                 55038595 
                 tripartite motif- 
               
               
                   
                   
                   
                   
                   
                 containing protein 48 
               
               
                 TRPM8 
                 NM_024080 
                 chr2 
                 234826042 
                 234928166 
                 transient receptor 
               
               
                   
                   
                   
                   
                   
                 potential cation channel 
               
               
                   
                   
                   
                   
                   
                 subfamily M member 8 
               
               
                 TSPAN9 
                 NM_001168320 
                 chr12 
                 3186520 
                 3395730 
                 tetraspanin-9 
               
               
                 TTF1 
                 NM_001205296 
                 chr9 
                 135250936 
                 135282238 
                 transcription termination 
               
               
                   
                   
                   
                   
                   
                 factor 1 isoform 2 
               
               
                 VPS8 
                 NM_015303 
                 chr3 
                 184529930 
                 184770402 
                 vacuolar protein sorting- 
               
               
                   
                   
                   
                   
                   
                 associated protein 8 
               
               
                   
                   
                   
                   
                   
                 homolog isoform b 
               
               
                 WASF3 
                 NM_001291965 
                 chr13 
                 27131839 
                 27263082 
                 wiskott-Aldrich 
               
               
                   
                   
                   
                   
                   
                 syndrome protein family 
               
               
                   
                   
                   
                   
                   
                 member 3 isoform 2 
               
               
                 WBSCR16 
                 NM_001281441 
                 chr7 
                 74470621 
                 74489717 
                 Williams-Beuren 
               
               
                   
                   
                   
                   
                   
                 syndrome chromosomal 
               
               
                   
                   
                   
                   
                   
                 region 16 protein 
               
               
                   
                   
                   
                   
                   
                 isoform 3 
               
               
                 WDFY3 
                 NM_014991 
                 chr4 
                 85590692 
                 85887544 
                 WD repeat and FYVE 
               
               
                   
                   
                   
                   
                   
                 domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 3 
               
               
                 WISP1 
                 NM_080838 
                 chr8 
                 134203281 
                 134243932 
                 WNT1-inducible- 
               
               
                   
                   
                   
                   
                   
                 signaling pathway 
               
               
                   
                   
                   
                   
                   
                 protein 1 isoform 2 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 XRCC5 
                 NM_021141 
                 chr2 
                 216974019 
                 217071016 
                 X-ray repair cross- 
               
               
                   
                   
                   
                   
                   
                 complementing protein 5 
               
               
                 YEATS2 
                 NM_018023 
                 chr3 
                 183415605 
                 183530413 
                 YEATS domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 2 
               
               
                 ZNF274 
                 NM_133502 
                 chr19 
                 58694355 
                 58724928 
                 neurotrophin receptor- 
               
               
                   
                   
                   
                   
                   
                 interacting factor 
               
               
                   
                   
                   
                   
                   
                 homolog isoform c 
               
               
                 ZNF702P 
                 NR_003578 
                 chr19 
                 53471503 
                 53496784 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 14 
               
             
            
               
                   
               
               
                 Genes with high expression in GSE9899 and CN-invariant in TCGA EOC samples 
               
            
           
           
               
               
               
               
               
               
            
               
                 Symbol 
                 Refseq 
                 Chr 
                 Start 
                 End 
                 Description 
               
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 ABCB4 
                 NM_018849 
                 chr7 
                 87031360 
                 87105019 
                 multidrug resistance 
               
               
                   
                   
                   
                   
                   
                 protein 3 isoform B 
               
               
                 ABHD5 
                 NM_016006 
                 chr3 
                 43732374 
                 43764217 
                 1-acylglycerol-3- 
               
               
                   
                   
                   
                   
                   
                 phosphate O- 
               
               
                   
                   
                   
                   
                   
                 acyltransferase ABHD5 
               
               
                 ACYP2 
                 NM_138448 
                 chr2 
                 54342409 
                 54532435 
                 acylphosphatase-2 
               
               
                 AFF3 
                 NM_001025108 
                 chr2 
                 100163715 
                 100722045 
                 AF4/FMR2 family 
               
               
                   
                   
                   
                   
                   
                 member 3 isoform 2 
               
               
                 AGAP1 
                 NM_001244888 
                 chr2 
                 236402732 
                 236761846 
                 arf-GAP with GTPase, 
               
               
                   
                   
                   
                   
                   
                 ANK repeat and PH 
               
               
                   
                   
                   
                   
                   
                 domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 1 isoform 3 
               
               
                 AMD1 
                 NM_001287216 
                 chr6 
                 111195986 
                 111216915 
                 S-adenosylmethionine 
               
               
                   
                   
                   
                   
                   
                 decarboxylase 
               
               
                   
                   
                   
                   
                   
                 proenzyme isoform 5 
               
               
                 ANK2 
                 NM_001127493 
                 chr4 
                 113739238 
                 114304896 
                 ankyrin-2 isoform 3 
               
               
                 ARSE 
                 NM_001282628 
                 chrX 
                 2852672 
                 2882494 
                 arylsulfatase E isoform 1 
               
               
                 ASAP1 
                 NM_018482 
                 chr8 
                 131064350 
                 131455906 
                 arf-GAP with SH3 
               
               
                   
                   
                   
                   
                   
                 domain, ANK repeat 
               
               
                   
                   
                   
                   
                   
                 and PH domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 1 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 ASCC3 
                 NM_001284271 
                 chr6 
                 101163006 
                 101329248 
                 activating signal 
               
               
                   
                   
                   
                   
                   
                 cointegrator 1 complex 
               
               
                   
                   
                   
                   
                   
                 subunit 3 isoform c 
               
               
                 ATAD2B 
                 NM_001242338 
                 chr2 
                 23971533 
                 24149984 
                 ATPase family AAA 
               
               
                   
                   
                   
                   
                   
                 domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 2B isoform 2 
               
               
                 ATF7IP2 
                 NM_024997 
                 chr16 
                 10479911 
                 10577495 
                 activating transcription 
               
               
                   
                   
                   
                   
                   
                 factor 7-interacting 
               
               
                   
                   
                   
                   
                   
                 protein 2 isoform 1 
               
               
                 ATXN7 
                 NM_001128149 
                 chr3 
                 63953419 
                 63989136 
                 ataxin-7 isoform c 
               
               
                 AUTS2 
                 NM_015570 
                 chr7 
                 69063904 
                 70258054 
                 autism susceptibility 
               
               
                   
                   
                   
                   
                   
                 gene 2 protein isoform 1 
               
               
                 BATF3 
                 NM_018664 
                 chr1 
                 212859758 
                 212873327 
                 basic leucine zipper 
               
               
                   
                   
                   
                   
                   
                 transcriptional factor 
               
               
                   
                   
                   
                   
                   
                 ATF-like 3 
               
               
                 BMPR2 
                 NM_001204 
                 chr2 
                 203241049 
                 203432474 
                 bone morphogenetic 
               
               
                   
                   
                   
                   
                   
                 protein receptor type-2 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 BTNL8 
                 NM_001159707 
                 chr5 
                 180326076 
                 180377906 
                 butyrophilin-like protein 
               
               
                   
                   
                   
                   
                   
                 8 isoform 3 precursor 
               
               
                 C1orf21 
                 NM_030806 
                 chr1 
                 184356149 
                 184598155 
                 uncharacterized protein 
               
               
                   
                   
                   
                   
                   
                 C1orf21 
               
               
                 CACNB2 
                 NM_201571 
                 chr10 
                 18429741 
                 18830688 
                 voltage-dependent L- 
               
               
                   
                   
                   
                   
                   
                 type calcium channel 
               
               
                   
                   
                   
                   
                   
                 subunit beta-2 isoform 6 
               
               
                 CAMTA1 
                 NR_038934 
                 chr1 
                 6845383 
                 6948261 
               
               
                 CASC5 
                 NM_170589 
                 chr15 
                 40886446 
                 40954881 
                 protein CASC5 isoform 1 
               
               
                 CASQ2 
                 NM_001232 
                 chr1 
                 116242625 
                 116311426 
                 calsequestrin-2 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 CCDC88A 
                 NM_018084 
                 chr2 
                 55514977 
                 55647057 
                 girdin isoform 2 
               
               
                 CHL1 
                 NR_045572 
                 chr3 
                 239325 
                 290282 
               
               
                 CHST15 
                 NM_014863 
                 chr10 
                 125779168 
                 125851940 
                 carbohydrate 
               
               
                   
                   
                   
                   
                   
                 sulfotransferase 15 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 CLASP1 
                 NM_001142273 
                 chr2 
                 122095351 
                 122407052 
                 CLIP-associating 
               
               
                   
                   
                   
                   
                   
                 protein 1 isoform 2 
               
               
                 CLIC4 
                 NM_013943 
                 chr1 
                 25071759 
                 25170815 
                 chloride intracellular 
               
               
                   
                   
                   
                   
                   
                 channel protein 4 
               
               
                 CLMN 
                 NM_024734 
                 chr14 
                 95648275 
                 95786245 
                 calmin 
               
               
                 COPA 
                 NM_001098398 
                 chr1 
                 160258376 
                 160313354 
                 coatomer subunit alpha 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 CUL3 
                 NM_001257197 
                 chr2 
                 225334866 
                 225450114 
                 cullin-3 isoform 2 
               
               
                 DAB1 
                 NM_021080 
                 chr1 
                 57463578 
                 58716211 
                 disabled homolog 1 
               
               
                 DAPK1 
                 NM_001288729 
                 chr9 
                 90113449 
                 90323549 
                 death-associated protein 
               
               
                   
                   
                   
                   
                   
                 kinase 1 
               
               
                 DDAH1 
                 NM_012137 
                 chr1 
                 85784167 
                 85930889 
                 N(G),N(G)- 
               
               
                   
                   
                   
                   
                   
                 dimethylarginine 
               
               
                   
                   
                   
                   
                   
                 dimethylaminohydrolase 
               
               
                   
                   
                   
                   
                   
                 1 isoform 1 
               
               
                 DEGS1 
                 NM_003676 
                 chr1 
                 224370909 
                 224381142 
                 sphingolipid delta(4)- 
               
               
                   
                   
                   
                   
                   
                 desaturase DES1 
               
               
                 DEPDC1 
                 NM_001114120 
                 chr1 
                 68939834 
                 68962904 
                 DEP domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 1A isoform a 
               
               
                 DNM3 
                 NM_015569 
                 chr1 
                 171810617 
                 172381857 
                 dynamin-3 isoform a 
               
               
                 DPPA4 
                 NM_018189 
                 chr3 
                 109044987 
                 109056419 
                 developmental 
               
               
                   
                   
                   
                   
                   
                 pluripotency-associated 
               
               
                   
                   
                   
                   
                   
                 protein 4 
               
               
                 DYRK1A 
                 NM_001396 
                 chr21 
                 38792601 
                 38887679 
                 dual specificity tyrosine- 
               
               
                   
                   
                   
                   
                   
                 phosphorylation- 
               
               
                   
                   
                   
                   
                   
                 regulated kinase 1A 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 EFHC2 
                 NM_025184 
                 chrX 
                 44007127 
                 44202923 
                 EF-hand domain- 
               
               
                   
                   
                   
                   
                   
                 containing family 
               
               
                   
                   
                   
                   
                   
                 member C2 
               
               
                 EHBP1 
                 NM_015252 
                 chr2 
                 62933000 
                 63273621 
                 EH domain-binding 
               
               
                   
                   
                   
                   
                   
                 protein 1 isoform 1 
               
               
                 EHD3 
                 NM_014600 
                 chr2 
                 31456879 
                 31491260 
                 EH domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 3 
               
               
                 EIF5 
                 NM_001969 
                 chr14 
                 103800338 
                 103811361 
                 eukaryotic translation 
               
               
                   
                   
                   
                   
                   
                 initiation factor 5 
               
               
                 ENPP2 
                 NR_045555 
                 chr8 
                 120569316 
                 120605248 
               
               
                 EPB41 
                 NM_001166007 
                 chr1 
                 29213602 
                 29446558 
                 protein 4.1 isoform 5 
               
               
                 EPHB2 
                 NM_004442 
                 chr1 
                 23037330 
                 23241823 
                 ephrin type-B receptor 2 
               
               
                   
                   
                   
                   
                   
                 isoform 2 precursor 
               
               
                 ERBB4 
                 NM_005235 
                 chr2 
                 212240441 
                 213403352 
                 receptor tyrosine-protein 
               
               
                   
                   
                   
                   
                   
                 kinase erbB-4 isoform 
               
               
                   
                   
                   
                   
                   
                 JM-a/CVT-1 precursor 
               
               
                 ERC2 
                 NM_015576 
                 chr3 
                 55542335 
                 56502391 
                 ERC protein 2 
               
               
                 ESRRG 
                 NM_206594 
                 chr1 
                 216676587 
                 217262987 
                 estrogen-related 
               
               
                   
                   
                   
                   
                   
                 receptor gamma isoform 2 
               
               
                 FAHD2A 
                 NM_016044 
                 chr2 
                 96068447 
                 96078879 
                 fumarylacetoacetate 
               
               
                   
                   
                   
                   
                   
                 hydrolase domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 2A 
               
               
                 FAM49A 
                 NM_030797 
                 chr2 
                 16730729 
                 16847134 
                 protein FAM49A 
               
               
                 FAT1 
                 NM_005245 
                 chr4 
                 187508936 
                 187644987 
                 protocadherin Fat 1 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 FCGR2A 
                 NM_001136219 
                 chr1 
                 161475204 
                 161489360 
                 low affinity 
               
               
                   
                   
                   
                   
                   
                 immunoglobulin gamma 
               
               
                   
                   
                   
                   
                   
                 Fc region receptor II-a 
               
               
                   
                   
                   
                   
                   
                 isoform 1 precursor 
               
               
                 FGF12 
                 NM_004113 
                 chr3 
                 191857181 
                 192445388 
                 fibroblast growth factor 
               
               
                   
                   
                   
                   
                   
                 12 isoform 2 
               
               
                 FGGY 
                 NM_001113411 
                 chr1 
                 59762624 
                 60228402 
                 FGGY carbohydrate 
               
               
                   
                   
                   
                   
                   
                 kinase domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 
               
               
                   
                   
                   
                   
                   
                 isoform a 
               
               
                 FHIT 
                 NM_002012 
                 chr3 
                 59735035 
                 61237133 
                 bis(5′-adenosyl)- 
               
               
                   
                   
                   
                   
                   
                 triphosphatase 
               
               
                 FHL1 
                 NM_001159702 
                 chrX 
                 135229558 
                 135293518 
                 four and a half LIM 
               
               
                   
                   
                   
                   
                   
                 domains protein 1 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 FHL2 
                 NM_201557 
                 chr2 
                 105977282 
                 106055230 
                 four and a half LIM 
               
               
                   
                   
                   
                   
                   
                 domains protein 2 
               
               
                 FUT9 
                 NM_006581 
                 chr6 
                 96463844 
                 96663488 
                 alpha-(1,3)- 
               
               
                   
                   
                   
                   
                   
                 fucosyltransferase 9 
               
               
                 GAP43 
                 NM_002045 
                 chr3 
                 115342150 
                 115440334 
                 neuromodulin isoform 2 
               
               
                 GBE1 
                 NM_000158 
                 chr3 
                 81538849 
                 81810950 
                 1,4-alpha-glucan- 
               
               
                   
                   
                   
                   
                   
                 branching enzyme 
               
               
                 GLI2 
                 NM_005270 
                 chr2 
                 121554866 
                 121750229 
                 zinc finger protein GLI2 
               
               
                 GOLIM4 
                 NM_014498 
                 chr3 
                 167727653 
                 167813417 
                 Golgi integral 
               
               
                   
                   
                   
                   
                   
                 membrane protein 4 
               
               
                 GPBP1L1 
                 NM_021639 
                 chr1 
                 46092975 
                 46152302 
                 vasculin-like protein 1 
               
               
                 GRM8 
                 NM_001127323 
                 chr7 
                 126078651 
                 126892428 
                 metabotropic glutamate 
               
               
                   
                   
                   
                   
                   
                 receptor 8 isoform b 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 GTF2F2 
                 NM_004128 
                 chr13 
                 45694630 
                 45858239 
                 general transcription 
               
               
                   
                   
                   
                   
                   
                 factor IIF subunit 2 
               
               
                 H6PD 
                 NM_001282587 
                 chr1 
                 9299902 
                 9331394 
                 GDH/6PGL 
               
               
                   
                   
                   
                   
                   
                 endoplasmic 
               
               
                   
                   
                   
                   
                   
                 bifunctional protein 
               
               
                   
                   
                   
                   
                   
                 isoform 1 precursor 
               
               
                 HHAT 
                 NM_001122834 
                 chr1 
                 210501595 
                 210849638 
                 protein-cysteine N- 
               
               
                   
                   
                   
                   
                   
                 palmitoyltransferase 
               
               
                   
                   
                   
                   
                   
                 HHAT isoform 1 
               
               
                 HS3ST1 
                 NM_005114 
                 chr4 
                 11399987 
                 11430537 
                 heparan sulfate 
               
               
                   
                   
                   
                   
                   
                 glucosamine 3-O- 
               
               
                   
                   
                   
                   
                   
                 sulfotransferase 1 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 HTR4 
                 NM_199453 
                 chr5 
                 147830594 
                 148016624 
                 5-hydroxytryptamine 
               
               
                   
                   
                   
                   
                   
                 receptor 4 isoform g 
               
               
                 HYAL3 
                 NM_003549 
                 chr3 
                 50330258 
                 50336899 
                 hyaluronidase-3 isoform 
               
               
                   
                   
                   
                   
                   
                 1 precursor 
               
               
                 IL15 
                 NR_037840 
                 chr4 
                 142557748 
                 142655140 
               
               
                 IL5RA 
                 NM_175726 
                 chr3 
                 3108007 
                 3152058 
                 interleukin-5 receptor 
               
               
                   
                   
                   
                   
                   
                 subunit alpha isoform 1 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 KCNAB1 
                 NM_172159 
                 chr3 
                 156008775 
                 156256927 
                 voltage-gated potassium 
               
               
                   
                   
                   
                   
                   
                 channel subunit beta-1 
               
               
                   
                   
                   
                   
                   
                 isoform 3 
               
               
                 LAMC3 
                 NM_006059 
                 chr9 
                 133884503 
                 133968446 
                 laminin subunit gamma- 
               
               
                   
                   
                   
                   
                   
                 3 precursor 
               
               
                 LDB2 
                 NM_001290 
                 chr4 
                 16503164 
                 16900424 
                 LIM domain-binding 
               
               
                   
                   
                   
                   
                   
                 protein 2 isoform a 
               
               
                 LEF1 
                 NM_001130714 
                 chr4 
                 108968700 
                 109090112 
                 lymphoid enhancer- 
               
               
                   
                   
                   
                   
                   
                 binding factor 1 isoform 3 
               
               
                 LPHN3 
                 NM_015236 
                 chr4 
                 62362838 
                 62938168 
                 latrophilin-3 precursor 
               
               
                 LRCH1 
                 NM_015116 
                 chr13 
                 47127295 
                 47319036 
                 leucine-rich repeat and 
               
               
                   
                   
                   
                   
                   
                 calponin homology 
               
               
                   
                   
                   
                   
                   
                 domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 1 isoform 2 
               
               
                 LRP1B 
                 NM_018557 
                 chr2 
                 140988995 
                 142889270 
                 low-density lipoprotein 
               
               
                   
                   
                   
                   
                   
                 receptor-related protein 
               
               
                   
                   
                   
                   
                   
                 1B precursor 
               
               
                 LYST 
                 NM_001301365 
                 chr1 
                 235824330 
                 236047008 
                 lysosomal-trafficking 
               
               
                   
                   
                   
                   
                   
                 regulator 
               
               
                 MAN1A1 
                 NM_005907 
                 chr6 
                 119498365 
                 119670931 
                 mannosyl- 
               
               
                   
                   
                   
                   
                   
                 oligosaccharide 1,2- 
               
               
                   
                   
                   
                   
                   
                 alpha-mannosidase IA 
               
               
                 MCTP1 
                 NM_001002796 
                 chr5 
                 94041241 
                 94417570 
                 multiple C2 and 
               
               
                   
                   
                   
                   
                   
                 transmembrane domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 1 
               
               
                   
                   
                   
                   
                   
                 isoform S 
               
               
                 MFAP3L 
                 NM_021647 
                 chr4 
                 170907747 
                 170947581 
                 microfibrillar-associated 
               
               
                   
                   
                   
                   
                   
                 protein 3-like isoform 1 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 MORC3 
                 NM_015358 
                 chr21 
                 37692486 
                 37748944 
                 MORC family CW-type 
               
               
                   
                   
                   
                   
                   
                 zinc finger protein 3 
               
               
                 MTA1 
                 NM_001203258 
                 chr14 
                 105886185 
                 105937057 
                 metastasis-associated 
               
               
                   
                   
                   
                   
                   
                 protein MTA1 isoform 
               
               
                   
                   
                   
                   
                   
                 MTA1s 
               
               
                 NECAP2 
                 NM_001145278 
                 chr1 
                 16767166 
                 16786584 
                 adaptin ear-binding 
               
               
                   
                   
                   
                   
                   
                 coat-associated protein 2 
               
               
                   
                   
                   
                   
                   
                 isoform 3 
               
               
                 NEIL3 
                 NM_018248 
                 chr4 
                 178230990 
                 178284092 
                 endonuclease 8-like 3 
               
               
                 NLGN4X 
                 NM_181332 
                 chrX 
                 5808066 
                 6146923 
                 neuroligin-4, X-linked 
               
               
                 NMD3 
                 NM_015938 
                 chr3 
                 160939098 
                 160969795 
                 60S ribosomal export 
               
               
                   
                   
                   
                   
                   
                 protein NMD3 
               
               
                 NOTCH2 
                 NM_024408 
                 chr1 
                 120454175 
                 120612317 
                 neurogenic locus notch 
               
               
                   
                   
                   
                   
                   
                 homolog protein 2 
               
               
                   
                   
                   
                   
                   
                 isoform 1 preproprotein 
               
               
                 NRP2 
                 NM_018534 
                 chr2 
                 206547223 
                 206641880 
                 neuropilin-2 isoform 4 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 NRXN1 
                 NM_004801 
                 chr2 
                 50145642 
                 51259674 
                 neurexin-1-beta isoform 
               
               
                   
                   
                   
                   
                   
                 alpha1 precursor 
               
               
                 NT5C2 
                 NM_001134373 
                 chr10 
                 104847773 
                 104953063 
                 cytosolic purine 5′- 
               
               
                   
                   
                   
                   
                   
                 nucleotidase 
               
               
                 NTNG1 
                 NM_014917 
                 chr1 
                 107682744 
                 108024475 
                 netrin-G1 isoform 3 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 NUP133 
                 NM_018230 
                 chr1 
                 229577043 
                 229644088 
                 nuclear pore complex 
               
               
                   
                   
                   
                   
                   
                 protein Nup133 
               
               
                 PARN 
                 NM_001134477 
                 chr16 
                 14529556 
                 14724128 
                 poly(A)-specific 
               
               
                   
                   
                   
                   
                   
                 ribonuclease PARN 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 PCDH7 
                 NM_032456 
                 chr4 
                 30722029 
                 30726957 
                 protocadherin-7 isoform 
               
               
                   
                   
                   
                   
                   
                 b precursor 
               
               
                 PCOLCE2 
                 NM_013363 
                 chr3 
                 142536701 
                 142608045 
                 procollagen C- 
               
               
                   
                   
                   
                   
                   
                 endopeptidase enhancer 
               
               
                   
                   
                   
                   
                   
                 2 precursor 
               
               
                 PDE2A 
                 NM_001146209 
                 chr11 
                 72287183 
                 72380108 
                 cGMP-dependent 3′,5′- 
               
               
                   
                   
                   
                   
                   
                 cyclic 
               
               
                   
                   
                   
                   
                   
                 phosphodiesterase 
               
               
                   
                   
                   
                   
                   
                 isoform PDE2A4 
               
               
                 PDE6C 
                 NM_006204 
                 chr10 
                 95372344 
                 95425429 
                 cone cGMP-specific 
               
               
                   
                   
                   
                   
                   
                 3′,5′-cyclic 
               
               
                   
                   
                   
                   
                   
                 phosphodiesterase 
               
               
                   
                   
                   
                   
                   
                 subunit alpha′ 
               
               
                 PDIA3 
                 NM_005313 
                 chr15 
                 44038589 
                 44064804 
                 protein disulfide- 
               
               
                   
                   
                   
                   
                   
                 isomerase A3 precursor 
               
               
                 PDZK1 
                 NM_001201325 
                 chr1 
                 145727665 
                 145764206 
                 Na(+)/H(+) exchange 
               
               
                   
                   
                   
                   
                   
                 regulatory cofactor 
               
               
                   
                   
                   
                   
                   
                 NHE-RF3 isoform 1 
               
               
                 PHTF1 
                 NM_006608 
                 chr1 
                 114239823 
                 114301777 
                 putative homeodomain 
               
               
                   
                   
                   
                   
                   
                 transcription factor 1 
               
               
                 PLEKHA2 
                 NM_021623 
                 chr8 
                 38758752 
                 38831430 
                 pleckstrin homology 
               
               
                   
                   
                   
                   
                   
                 domain-containing 
               
               
                   
                   
                   
                   
                   
                 family A member 2 
               
               
                 POU2F1 
                 NM_001198783 
                 chr1 
                 167298280 
                 167396582 
                 POU domain, class 2, 
               
               
                   
                   
                   
                   
                   
                 transcription factor 1 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 PRDM16 
                 NM_022114 
                 chr1 
                 2985741 
                 3355185 
                 PR domain zinc finger 
               
               
                   
                   
                   
                   
                   
                 protein 16 isoform 1 
               
               
                 PRDM5 
                 NM_001300824 
                 chr4 
                 121613067 
                 121844021 
                 PR domain zinc finger 
               
               
                   
                   
                   
                   
                   
                 protein 5 isfoorm 3 
               
               
                 PRKCE 
                 NM_005400 
                 chr2 
                 45879042 
                 46415129 
                 protein kinase C epsilon 
               
               
                   
                   
                   
                   
                   
                 type 
               
               
                 PRKCZ 
                 NM_001033582 
                 chr1 
                 2036154 
                 2116834 
                 protein kinase C zeta 
               
               
                   
                   
                   
                   
                   
                 type isoform 2 
               
               
                 PRUNE 
                 NM_021222 
                 chr1 
                 150980972 
                 151008189 
                 protein prune homolog 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 PTGS2 
                 NM_000963 
                 chr1 
                 186640943 
                 186649559 
                 prostaglandin G/H 
               
               
                   
                   
                   
                   
                   
                 synthase 2 precursor 
               
               
                 PTPRF 
                 NM_130440 
                 chr1 
                 43996546 
                 44089343 
                 receptor-type tyrosine- 
               
               
                   
                   
                   
                   
                   
                 protein phosphatase F 
               
               
                   
                   
                   
                   
                   
                 isoform 2 precursor 
               
               
                 PTPRZ1 
                 NM_002851 
                 chr7 
                 121513158 
                 121702090 
                 receptor-type tyrosine- 
               
               
                   
                   
                   
                   
                   
                 protein phosphatase zeta 
               
               
                   
                   
                   
                   
                   
                 isoform 1 precursor 
               
               
                 PUM1 
                 NM_014676 
                 chr1 
                 31404352 
                 31538564 
                 pumilio homolog 1 
               
               
                   
                   
                   
                   
                   
                 isoform 2 
               
               
                 RAD52 
                 NM_001297419 
                 chr12 
                 1020901 
                 1099207 
                 DNA repair protein 
               
               
                   
                   
                   
                   
                   
                 RAD52 homolog 
               
               
                   
                   
                   
                   
                   
                 isoform a 
               
               
                 RAI2 
                 NM_001172743 
                 chrX 
                 17818168 
                 17879457 
                 retinoic acid-induced 
               
               
                   
                   
                   
                   
                   
                 protein 2 isoform 1 
               
               
                 RNF144A 
                 NM_014746 
                 chr2 
                 7057522 
                 7184309 
                 E3 ubiquitin-protein 
               
               
                   
                   
                   
                   
                   
                 ligase RNF144A 
               
               
                 SCHIP1 
                 NM_014575 
                 chr3 
                 158991035 
                 159615155 
                 schwannomin- 
               
               
                   
                   
                   
                   
                   
                 interacting protein 1 
               
               
                   
                   
                   
                   
                   
                 isoform 1 
               
               
                 SERTAD2 
                 NM_014755 
                 chr2 
                 64858754 
                 64881046 
                 SERTA domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 2 
               
               
                 SLC12A6 
                 NM_001042495 
                 chr15 
                 34522196 
                 34630265 
                 solute carrier family 12 
               
               
                   
                   
                   
                   
                   
                 member 6 isoform c 
               
               
                 SLC15A2 
                 NM_001145998 
                 chr3 
                 121613170 
                 121663034 
                 solute carrier family 15 
               
               
                   
                   
                   
                   
                   
                 member 2 isoform b 
               
               
                 SLC4A4 
                 NM_003759 
                 chr4 
                 72204769 
                 72437804 
                 electrogenic sodium 
               
               
                   
                   
                   
                   
                   
                 bicarbonate 
               
               
                   
                   
                   
                   
                   
                 cotransporter 1 isoform 2 
               
               
                 SMYD3 
                 NM_022743 
                 chr1 
                 245912641 
                 246580714 
                 histone-lysine N- 
               
               
                   
                   
                   
                   
                   
                 methyltransferase 
               
               
                   
                   
                   
                   
                   
                 SMYD3 isoform 2 
               
               
                 SNTG2 
                 NM_018968 
                 chr2 
                 946553 
                 1371384 
                 gamma-2-syntrophin 
               
               
                 SPATS2L 
                 NM_001100424 
                 chr2 
                 201170984 
                 201346986 
                 SPATS2-like protein 
               
               
                   
                   
                   
                   
                   
                 isoform b 
               
               
                 TBL1X 
                 NM_001139468 
                 chrX 
                 9431334 
                 9687780 
                 F-box-like/WD repeat- 
               
               
                   
                   
                   
                   
                   
                 containing protein 
               
               
                   
                   
                   
                   
                   
                 TBL1X isoform b 
               
               
                 TGFBR3 
                 NM_001195683 
                 chr1 
                 92145899 
                 92351836 
                 transforming growth 
               
               
                   
                   
                   
                   
                   
                 factor beta receptor type 
               
               
                   
                   
                   
                   
                   
                 3 isoform b precursor 
               
               
                 THRAP3 
                 NM_005119 
                 chr1 
                 36690016 
                 36770957 
                 thyroid hormone 
               
               
                   
                   
                   
                   
                   
                 receptor-associated 
               
               
                   
                   
                   
                   
                   
                 protein 3 
               
               
                 TIAM1 
                 NM_003253 
                 chr21 
                 32490735 
                 32931290 
                 T-lymphoma invasion 
               
               
                   
                   
                   
                   
                   
                 and metastasis-inducing 
               
               
                   
                   
                   
                   
                   
                 protein 1 
               
               
                 TLE4 
                 NM_007005 
                 chr9 
                 82186687 
                 82341796 
                 transducin-like enhancer 
               
               
                   
                   
                   
                   
                   
                 protein 4 isoform 3 
               
               
                 TNIK 
                 NM_001161561 
                 chr3 
                 170780291 
                 171178197 
                 TRAF2 and NCK- 
               
               
                   
                   
                   
                   
                   
                 interacting protein 
               
               
                   
                   
                   
                   
                   
                 kinase isoform 3 
               
               
                 TRIM48 
                 NM_024114 
                 chr11 
                 55029657 
                 55038595 
                 tripartite motif- 
               
               
                   
                   
                   
                   
                   
                 containing protein 48 
               
               
                 TRPM8 
                 NM_024080 
                 chr2 
                 234826042 
                 234928166 
                 transient receptor 
               
               
                   
                   
                   
                   
                   
                 potential cation channel 
               
               
                   
                   
                   
                   
                   
                 subfamily M member 8 
               
               
                 TSPAN9 
                 NM_001168320 
                 chr12 
                 3186520 
                 3395730 
                 tetraspanin-9 
               
               
                 TTF1 
                 NM_001205296 
                 chr9 
                 135250936 
                 135282238 
                 transcription termination 
               
               
                   
                   
                   
                   
                   
                 factor 1 isoform 2 
               
               
                 VPS8 
                 NM_015303 
                 chr3 
                 184529930 
                 184770402 
                 vacuolar protein sorting- 
               
               
                   
                   
                   
                   
                   
                 associated protein 8 
               
               
                   
                   
                   
                   
                   
                 homolog isoform b 
               
               
                 WASF3 
                 NM_001291965 
                 chr13 
                 27131839 
                 27263082 
                 wiskott-Aldrich 
               
               
                   
                   
                   
                   
                   
                 syndrome protein family 
               
               
                   
                   
                   
                   
                   
                 member 3 isoform 2 
               
               
                 WBSCR16 
                 NM_001281441 
                 chr7 
                 74470621 
                 74489717 
                 Williams-Beuren 
               
               
                   
                   
                   
                   
                   
                 syndrome chromosomal 
               
               
                   
                   
                   
                   
                   
                 region 16 protein 
               
               
                   
                   
                   
                   
                   
                 isoform 3 
               
               
                 WDFY3 
                 NM_014991 
                 chr4 
                 85590692 
                 85887544 
                 WD repeat and FYVE 
               
               
                   
                   
                   
                   
                   
                 domain-containing 
               
               
                   
                   
                   
                   
                   
                 protein 3 
               
               
                 WISP1 
                 NM_080838 
                 chr8 
                 134203281 
                 134243932 
                 WNT1-inducible- 
               
               
                   
                   
                   
                   
                   
                 signaling pathway 
               
               
                   
                   
                   
                   
                   
                 protein 1 isoform 2 
               
               
                   
                   
                   
                   
                   
                 precursor 
               
               
                 XRCC5 
                 NM_021141 
                 chr2 
                 216974019 
                 217071016 
                 X-ray repair cross- 
               
               
                   
                   
                   
                   
                   
                 complementing protein 5 
               
               
                 YEATS2 
                 NM_018023 
                 chr3 
                 183415605 
                 183530413 
                 YEATS domain- 
               
               
                   
                   
                   
                   
                   
                 containing protein 2 
               
               
                 ZNF274 
                 NM_133502 
                 chr19 
                 58694355 
                 58724928 
                 neurotrophin receptor- 
               
               
                   
                   
                   
                   
                   
                 interacting factor 
               
               
                   
                   
                   
                   
                   
                 homolog isoform c 
               
               
                 ZNF702P 
                 NR_003578 
                 chr19 
                 53471503 
                 53496784 
               
               
                   
               
            
           
         
       
     
     REFERENCES 
     
         
         Abecasis G R, Altshuler D, Auton A, Brooks L D, Durbin R M, et al. (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073. 
         Assmann G, Schulte H (1988) The prospective cardiovascular münster (procam) study: prevalence of hyperlipidemia in persons with hypertension and/or diabetes mellitus and the relationship to coronary heart disease. American heart journal 116: 1713-24. 
         Bell D, Berchuck A, Birrer M, Chien J, Cramer D, et al. (2011) Integrated genomic analyses of ovarian carcinoma. Nature 474: 609-15. 
         Benjamin E J, Wolf P A, D&#39;Agostino R B, Silbershatz H, Kannel W B, et al. (1998) Impact of atrial fibrillation on the risk of death: the framingham heart study. Circulation 98: 946-52. 
         Church D M, Schneider V A, Graves T, Auger K, Cunningham F, et al. (2011) Modernizing reference genome assemblies. PLoS biology 9: 1001091. 
         Mills R E, Walter K, Stewart C, Handsaker R E, Chen K, et al. (2011) Mapping copy number variation by population-scale genome sequencing. Nature 470: 59-65. 
         Motakis E, Ivshina A V, Kuznetsov V A (2009) Data-driven approach to predict survival of cancer patients: estimation of microarray genes&#39; prediction significance by cox proportional hazard regression model. IEEE Eng Med Biol Mag 28: 58-66. 
         Tothill R W, Tinker A V, George J, Brown R, Fox S B, et al. (2008) Novel molecular subtypes of serous and endometrioid ovarian cancer linked to clinical outcome. Clin Cancer Res 14: 5198-5208.