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["Probe set name","Gene symbol","Annotation","t-statistic"]
["204703_at","IFT88","This gene encodes a member of the tetratrico peptide repeat (TPR) family. Mutations of a similar gene in mouse can cause polycystic kidney disease. Two transcript variants encoding distinct isoforms have been identified for this gene. Diseases associated with IFT88 include orofaciodigital syndrome i and polycystic kidney disease. Among its related pathways are Signaling by GPCR and Organelle biogenesis and maintenance. GO annotations related to this gene include kinesin binding.    1. Kuehn et. al. von Hippel-Lindau: A Tumor Suppressor Links Microtubules to Ciliogenesis and Cancer Development",8.704]
["205441_at","OCEL1","Not much information available about this gene (surprising!)     1. Neilsen et. Al. Mutant p53 uses p63 as a molecular chaperone to alter gene expression and induce a pro-invasive secretome",8.421]
["201930_at","MCM6","MCM6 is one of the highly conserved mini-chromosome maintenance proteins (MCM) that are essential for the initiation of eukaryotic genome replication.   Link to breast cancer: 1. Van't Veer, Laura J., et al. \"Gene expression profiling predicts clinical outcome of breast cancer.\" nature 415.6871 (2002): 530-536. 2. Sotiriou, Christos, et al. \"Breast cancer classification and prognosis based on gene expression profiles from a population-based study.\" Proceedings of the National Academy of Sciences 100.18 (2003): 10393-10398.",-7.983]
["208628_s_at","YBX1","YBX1 (Y Box Binding Protein 1) is a Protein Coding gene. Diseases associated with YBX1 include liposarcoma and breast cancer. Among its related pathways are Signaling events mediated by PTP1B and Translational Control. GO annotations related to this gene include nucleic acid binding and transcription factor activity, sequence-specific DNA binding. An important paralog of this gene is YBX2.       1. Stratford, Anna L., et al. \"Y-box binding protein-1 serine 102 is a downstream target of p90 ribosomal S6 kinase in basal-like breast cancer cells.\" Breast Cancer Res 10.6 (2008): R99.",-7.695]
["218437_s_at","LZTFL1","This gene encodes a ubiquitously expressed protein that localizes to the cytoplasm. This protein interacts with Bardet-Biedl Syndrome (BBS) proteins and, through its interaction with BBS protein complexes, regulates protein trafficking to the ciliary membrane. Nonsense mutations in this gene cause a form of Bardet-Biedl Syndrome; a ciliopathy characterized in part by polydactyly, obesity, cognitive impairment, hypogonadism, and kidney failure. This gene may also function as a tumor suppressor; possibly by interacting with E-cadherin and the actin cytoskeleton and thereby regulating the transition of epithelial cells to mesenchymal cells. Alternative splicing of this gene results in multiple transcript variants. Diseases associated with LZTFL1 include bardet-biedl syndrome 17 and lztfl1- related bardet-biedl syndrome. Among its related pathways are Organelle biogenesis and maintenance and Cargo trafficking to the periciliary membrane. GO annotations related to this gene include identical protein binding and protein complex binding.     1. Chanrion et. al. A Gene Expression Signature that Can Predict the Recurrence of Tamoxifen-Treated Primary Breast Cancer",7.646]
["212736_at","C16orf45","This gene has 11 transcripts (splice variants), 1 gene allele, 62 orthologues, is a member of 1 Ensembl protein family and is associated with 5 phenotypes. C16orf45 (Chromosome 16 Open Reading Frame 45) is a Protein Coding gene. Not much literature available.   1.Partheen et. al. Expression analysis of stage III serous ovarian adenocarcinoma distinguishes a sub-group of survivors. This is the only one I can find somewhat related (ovarian is unique for women)",7.249]
["206197_at","NME5","NME5 (NME/NM23 Family Member 5) is a Protein Coding gene. Among its related pathways are Carbon metabolism and Metabolism. GO annotations related to this gene include nucleoside diphosphate kinase activity. An important paralog of this gene is NME7. Does not seem to have NDK kinase activity. Confers protection from cell death by Bax and alters the cellular levels of several antioxidant enzymes including Gpx5. May play a role in spermiogenesis by increasing the ability of late-stage spermatids to eliminate reactive oxygen species (By similarity).     1. Parris et. al. Clinical Implications of Gene Dosage and Gene Expression Patterns in Diploid Breast Carcinoma",7.183]
["203554_x_at","PTTG1","PTTG1 (Pituitary Tumor-Transforming 1) is a Protein Coding gene. Diseases associated with PTTG1 include thymic hyperplasia and thyroid cancer, nonmedullary, 2. Among its related pathways are Cell Cycle, Mitotic and Integrated Pancreatic Cancer Pathway. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and cysteine-type endopeptidase inhibitor activity. An important paralog of this gene is PTTG2. Regulatory protein, which plays a central role in chromosome stability, in the p53/TP53 pathway, and DNA repair. Probably acts by blocking the action of key proteins. During the mitosis, it blocks Separase/ESPL1 function, preventing the proteolysis of the cohesin complex and the subsequent segregation of the chromosomes. At the onset of anaphase, it is ubiquitinated, conducting to its destruction and to the liberation of ESPL1. Its function is however not limited to a blocking activity, since it is required to activate ESPL1. Negatively regulates the transcriptional activity and related apoptosis activity of TP53. The negative regulation of TP53 may explain the strong transforming capability of the protein when it is overexpressed. May also play a role in DNA repair via its interaction with Ku, possibly by connecting DNA damage-response pathways with sister chromatid separation.     1. Ghayad et. al. Identification of TACC1, NOV, and PTTG1 as new candidate genes associated with endocrine therapy resistance in breast cancer",-7.147]
["203143_s_at","KIAA0040","Not much description about this gene      1. Peng et. al. Tumor-Associated Galectin-3 Modulates the Function of Tumor-Reactive T Cells; 2. Jenssen et. al. Associations between gene expressions in breast cancer and patient survival",7.078]
["202107_s_at","MCM2","The protein encoded by this gene is one of the highly conserved mini-chromosome maintenance proteins (MCM) that are involved in the initiation of eukaryotic genome replication. The hexameric protein complex formed by MCM proteins is a key component of the pre-replication complex (pre_RC) and may be involved in the formation of replication forks and in the recruitment of other DNA replication related proteins. This protein forms a complex with MCM4, 6, and 7, and has been shown to regulate the helicase activity of the complex. This protein is phosphorylated, and thus regulated by, protein kinases CDC2 and CDC7.    1. Perou et. al. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers; 2. Sotiriou et. al. Breast cancer classification and prognosis based on gene expression profiles from a population-based study",-7.037]
["213911_s_at","H2AFZ","Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Nucleosomes consist of approximately 146 bp of DNA wrapped around a histone octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. This gene encodes a replication-independent member of the histone H2A family that is distinct from other members of the family. Studies in mice have shown that this particular histone is required for embryonic development and indicate that lack of functional histone H2A leads to embryonic lethality.     1.Kreike et. al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas",-7.005]
["218692_at","SYBU","Syntabulin/GOLSYN is part of a kinesin motor-adaptor complex that is critical for the anterograde axonal transport of active zone components and contributes to activity-dependent presynaptic assembly during neuronal development. SYBU (Syntabulin (Syntaxin-Interacting)) is a Protein Coding gene. GO annotations related to this gene include microtubule binding and syntaxin-1 binding. An important paralog of this gene is SNPH.     1.Casa et. al. Estrogen and insulin-like growth factor-I (IGF-I) independently down-regulate critical repressors of breast cancer growth (29 cited, not many frequently cited papers)",7]
["204934_s_at","HPN","This gene encodes a type II transmembrane serine protease that may be involved in diverse cellular functions, including blood coagulation and the maintenance of cell morphology. Expression of the encoded protein is associated with the growth and progression of cancers, particularly prostate cancer. The protein is cleaved into a catalytic serine protease chain and a non-catalytic scavenger receptor cysteine-rich chain, which associate via a single disulfide bond. Alternative splicing results in multiple transcript variants. Diseases associated with HPN include prostate cancer. Among its related pathways are Viral carcinogenesis. GO annotations related to this gene include serine-type endopeptidase activity and serine-type peptidase activity.       1. Smirnov et. al. Global Gene Expression Profiling of Circulating Tumor Cells; 2. Tozlu et. al. Identification of novel genes that co-cluster with estrogen receptor alpha in breast tumor biopsy specimens, using a large-scale real-time reverse transcription-PCR approach",6.964]
["208627_s_at","YBX1","Same as previous",-6.96]
["201685_s_at","TOX4","TOX4 (TOX High Mobility Group Box Family Member 4) is a Protein Coding gene. Among its related pathways are NF-kappaB Signaling. GO annotations related to this gene include chromatin binding. An important paralog of this gene is SSRP1. Component of the PTW/PP1 phosphatase complex, which plays a role in the control of chromatin structure and cell cycle progression during the transition from mitosis into interphase.        1. Tessema et. al. Differential Epigenetic Regulation of TOX Subfamily High Mobility Group Box Genes in Lung and Breast Cancers",6.899]
["204045_at","TCEAL1","This gene encodes a member of the transcription elongation factor A (SII)-like (TCEAL) gene family. Members of this family may function as nuclear phosphoproteins that modulate transcription in a promoter context-dependent manner. The encoded protein is similar to transcription elongation factor A/transcription factor SII and contains a zinc finger-like motif as well as a sequence related to the transcription factor SII Pol II-binding region. It may exert its effects via protein-protein interactions with other transcriptional regulators rather than via direct binding of DNA. Multiple family members are located on the X chromosome. Alternative splicing results in multiple transcript variants encoding a single isoform. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding. An important paralog of this gene is WBP5.     1. Abba et. al. Gene expression signature of estrogen receptor α status in breast cancer",6.87]
["204962_s_at","CENPA","Centromeres are the differentiated chromosomal domains that specify the mitotic behavior of chromosomes. This gene encodes a centromere protein which contains a histone H3 related histone fold domain that is required for targeting to the centromere. Centromere protein A is proposed to be a component of a modified nucleosome or nucleosome-like structure in which it replaces 1 or both copies of conventional histone H3 in the (H3-H4)2 tetrameric core of the nucleosome particle. The protein is a replication-independent histone that is a member of the histone H3 family. Alternative splicing results in multiple transcript variants encoding distinct isoforms.         1.Sotiriou et. al. Gene Expression Profiling in Breast Cancer: Understanding the Molecular Basis of Histologic Grade To Improve Prognosis; 2. Ma et. al. Gene expression profiles of human breast cancer progression",-6.858]
["209625_at","PIGH","This gene encodes an endoplasmic reticulum associated protein that is involved in glycosylphosphatidylinositol (GPI)-anchor biosynthesis. The GPI anchor is a glycolipid found on many blood cells and which serves to anchor proteins to the cell surface. The protein encoded by this gene is a subunit of the GPI N-acetylglucosaminyl (GlcNAc) transferase that transfers GlcNAc to phosphatidylinositol (PI) on the cytoplasmic side of the endoplasmic reticulum. Among its related pathways are Transport to the Golgi and subsequent modification and Metabolism. GO annotations related to this gene include phosphatidylinositol N-acetylglucosaminyltransferase activity. Not much literature found.",6.856]
["212908_at","DNAJC16","DNAJC16 (DnaJ (Hsp40) Homolog, Subfamily C, Member 16) is a Protein Coding gene. An important paralog of this gene is DNAJC18.      1. Xu et. al. Merging microarray data from separate breast cancer studies provides a robust prognostic test",6.836]
["203368_at","CRELD1","This gene encodes a member of a subfamily of epidermal growth factor-related proteins. The encoded protein is characterized by a cysteine-rich with epidermal growth factor-like domain. This protein may function as a cell adhesion molecule. Mutations in this gene are the cause of atrioventricular septal defect. Alternate splicing results in multiple transcript variants. Diseases associated with CRELD1 include atrioventricular septal defect 2 and complete atrioventricular canal - fallot tetralogy. GO annotations related to this gene include calcium ion binding.     1. Dehan et. al. Chromosomal aberrations and gene expression profiles in non-small cell lung cancer",6.826]
["200934_at","DEK","This gene encodes a protein with one SAP domain. This protein binds to cruciform and superhelical DNA and induces positive supercoils into closed circular DNA, and is also involved in splice site selection during mRNA processing. Chromosomal aberrations involving this region, increased expression of this gene, and the presence of antibodies against this protein are all associated with various diseases. Two transcript variants encoding different isoforms have been found for this gene.     1.Bergamaschi et. al. Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer",-6.806]
["213101_s_at","ACTR3","The specific function of this gene has not yet been determined; however, the protein it encodes is known to be a major constituent of the ARP2/3 complex. This complex is located at the cell surface and is essential to cell shape and motility through lamellipodial actin assembly and protrusion. Three transcript variants encoding two different isoforms have been found for this gene. Diseases associated with ACTR3 include wiskott-aldrich syndrome. Among its related pathways are Immune System and Signaling by GPCR.   1. Siripurapu et. al. DBC2 Significantly Influences Cell-cycle, Apoptosis, Cytoskeleton and Membrane-trafficking Pathways",-6.776]
["221676_s_at","CORO1C","This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. Three transcript variants encoding two different isoforms have been found for this gene. Diseases associated with CORO1C include coronin-1a deficiency.    1. Chang et. al. Gene Expression Signature of Fibroblast Serum Response Predicts Human Cancer Progression: Similarities between Tumors and Wounds",-6.737]
["214039_s_at","LAPTM4B","Increased expression of LAPTM4B has been found in breast, liver, lung, ovarian, uterine, gastric cancers. Elevated LAPTM4B level contributes to chemotherapy resistance in breast cancer. It was found that overexpression of LAPTM4B causes anthracyclines (doxorubicin, daunorubicin, and epirubicin) resistance by retaining drug in the cytoplasm and decreasing nuclear localization of drug and drug induced DNA damage.      1.Li et. al. Amplification of LAPTM4B and YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer",-6.695]
["202705_at","CCNB2","Cyclin B2 is a member of the cyclin family, specifically the B-type cyclins. The B-type cyclins, B1 and B2, associate with p34cdc2 and are essential components of the cell cycle regulatory machinery. B1 and B2 differ in their subcellular localization. Cyclin B1 co-localizes with microtubules, whereas cyclin B2 is primarily associated with the Golgi region. Cyclin B2 also binds to transforming growth factor beta RII and thus cyclin B2/cdc2 may play a key role in transforming growth factor beta-mediated cell cycle control. Diseases associated with CCNB2 include anauxetic dysplasia and breast cancer. Among its related pathways are GPCR Pathway and Regulation of PLK1 Activity at G2/M Transition. GO annotations related to this gene include protein kinase binding. An important paralog of this gene is CCND2.        1. Bertucci et. al. Gene Expression Profiling for Molecular Characterization of Inflammatory Breast Cancer and Prediction of Response to Chemotherapy; 2. Oh et. al. Estrogen-Regulated Genes Predict Survival in Hormone Receptor–Positive Breast Cancers",-6.649]
["218147_s_at","GLT8D1","This gene encodes a member of the glycosyltransferase family. The specific function of this protein has not been determined. Alternative splicing results in multiple transcript variants of this gene. GO annotations related to this gene include transferase activity, transferring glycosyl groups. An important paralog of this gene is GLT8D2.       1. Li et. al. Identification of Novel Breast Cancer Subtype-Specific Biomarkers by Integrating Genomics Analysis of DNA Copy Number Aberrations and miRNA-mRNA Dual Expression Profiling",6.645]
["202870_s_at","CDC20","CDC20 appears to act as a regulatory protein interacting with several other proteins at multiple points in the cell cycle. It is required for two microtubule-dependent processes, nuclear movement prior to anaphase and chromosome separation.   1.Ein-Dor et. al. Outcome signature genes in breast cancer: is there a unique set? 2.Frasor et. al. Profiling of Estrogen Up- and Down-Regulated Gene Expression in Human Breast Cancer Cells: Insights into Gene Networks and Pathways Underlying Estrogenic Control of Proliferation and Cell Phenotype",-6.632]
["214077_x_at","MEIS3P1","This gene appears to be a retrotransposed pseudogene based on its lack of exons compared to other family members, one of which is found on chromosome 19 (MEIS3). It does appear to be transcribed and has an ORF that may encode a protein of similar size and sequence to that encoded by MEIS3. It may not be very biologically meaningful.",6.629]
["65517_at","AP1M2","This gene encodes a subunit of the heterotetrameric adaptor-related protein comlex 1 (AP-1), which belongs to the adaptor complexes medium subunits family. This protein is capable of interacting with tyrosine-based sorting signals. Alternative splicing results in multiple transcript variants. Diseases associated with AP1M2 include pain agnosia and agnosia. Among its related pathways are Immune System and Infectious disease. An important paralog of this gene is AP4M1.       1. Pilarsky et. al. Activation of Wnt signalling in stroma from pancreatic cancer identified by gene expression profiling; 2. Rohan et. al. Gene Expression Profiling Separates Chromophobe Renal Cell Carcinoma from Oncocytoma and Identifies Vesicular Transport and Cell Junction Proteins as Differentially Expressed Genes",6.625]
["200996_at","ACTR3","Same as previous",-6.611]

{"sheet":"Top30_medIQR","index":1,"n_rows":31,"n_cols":4,"rows_kept":31,"cut":false,"hidden":false,"merged":[]}
["Probe set name","Gene symbol","Annotation","t-statistic"]
["204703_at","IFT88","This gene encodes a member of the tetratrico peptide repeat (TPR) family. Mutations of a similar gene in mouse can cause polycystic kidney disease. Two transcript variants encoding distinct isoforms have been identified for this gene. Diseases associated with IFT88 include orofaciodigital syndrome i and polycystic kidney disease. Among its related pathways are Signaling by GPCR and Organelle biogenesis and maintenance. GO annotations related to this gene include kinesin binding.    1. Kuehn et. al. von Hippel-Lindau: A Tumor Suppressor Links Microtubules to Ciliogenesis and Cancer Development",8.53]
["205441_at","OCEL1","Not much information available about this gene (surprising!)     1. Neilsen et. Al. Mutant p53 uses p63 as a molecular chaperone to alter gene expression and induce a pro-invasive secretome",8.465]
["201930_at","MCM6","MCM6 is one of the highly conserved mini-chromosome maintenance proteins (MCM) that are essential for the initiation of eukaryotic genome replication.   Link to breast cancer: 1. Van't Veer, Laura J., et al. \"Gene expression profiling predicts clinical outcome of breast cancer.\" nature 415.6871 (2002): 530-536. 2. Sotiriou, Christos, et al. \"Breast cancer classification and prognosis based on gene expression profiles from a population-based study.\" Proceedings of the National Academy of Sciences 100.18 (2003): 10393-10398.",-7.884]
["206197_at","NME5","NME5 (NME/NM23 Family Member 5) is a Protein Coding gene. Among its related pathways are Carbon metabolism and Metabolism. GO annotations related to this gene include nucleoside diphosphate kinase activity. An important paralog of this gene is NME7. Does not seem to have NDK kinase activity. Confers protection from cell death by Bax and alters the cellular levels of several antioxidant enzymes including Gpx5. May play a role in spermiogenesis by increasing the ability of late-stage spermatids to eliminate reactive oxygen species (By similarity).     1. Parris et. al. Clinical Implications of Gene Dosage and Gene Expression Patterns in Diploid Breast Carcinoma",7.472]
["204063_s_at","ULK2","This gene encodes a protein that is similar to a serine/threonine kinase in C. elegans which is involved in axonal elongation. The structure of this protein is similar to the C. elegans protein in that both proteins have an N-terminal kinase domain, a central proline/serine rich (PS) domain, and a C-terminal (C) domain. The gene is located within the Smith-Magenis syndrome region on chromosome 17. Alternatively spliced transcript variants encoding the same protein have been identified. Among its related pathways are mTOR signalling and Translation Insulin regulation of translation. GO annotations related to this gene include transferase activity, transferring phosphorus-containing groups and protein tyrosine kinase activity. An important paralog of this gene is ULK3.      1. Ouyang et. al. MicroRNA Profiling Implies New Markers of Chemoresistance of Triple-Negative Breast Cancer; 2. Sabine et. al. Gene expression profiling of response to mTOR inhibitor everolimus in pre-operatively treated post-menopausal women with oestrogen receptor-positive breast cancer",7.388]
["212736_at","C16orf45","This gene has 11 transcripts (splice variants), 1 gene allele, 62 orthologues, is a member of 1 Ensembl protein family and is associated with 5 phenotypes. C16orf45 (Chromosome 16 Open Reading Frame 45) is a Protein Coding gene. Not much literature available.   1.Partheen et. al. Expression analysis of stage III serous ovarian adenocarcinoma distinguishes a sub-group of survivors. This is the only one I can find somewhat related (ovarian is unique for women)",7.338]
["218692_at","SYBU","Syntabulin/GOLSYN is part of a kinesin motor-adaptor complex that is critical for the anterograde axonal transport of active zone components and contributes to activity-dependent presynaptic assembly during neuronal development. SYBU (Syntabulin (Syntaxin-Interacting)) is a Protein Coding gene. GO annotations related to this gene include microtubule binding and syntaxin-1 binding. An important paralog of this gene is SNPH.     1.Casa et. al. Estrogen and insulin-like growth factor-I (IGF-I) independently down-regulate critical repressors of breast cancer growth (29 cited, not many frequently cited papers)",7.17]
["204962_s_at","CENPA","Centromeres are the differentiated chromosomal domains that specify the mitotic behavior of chromosomes. This gene encodes a centromere protein which contains a histone H3 related histone fold domain that is required for targeting to the centromere. Centromere protein A is proposed to be a component of a modified nucleosome or nucleosome-like structure in which it replaces 1 or both copies of conventional histone H3 in the (H3-H4)2 tetrameric core of the nucleosome particle. The protein is a replication-independent histone that is a member of the histone H3 family. Alternative splicing results in multiple transcript variants encoding distinct isoforms.         1.Sotiriou et. al. Gene Expression Profiling in Breast Cancer: Understanding the Molecular Basis of Histologic Grade To Improve Prognosis; 2. Ma et. al. Gene expression profiles of human breast cancer progression",-6.987]
["203143_s_at","KIAA0040","Not much description about this gene      1. Peng et. al. Tumor-Associated Galectin-3 Modulates the Function of Tumor-Reactive T Cells; 2. Jenssen et. al. Associations between gene expressions in breast cancer and patient survival",6.973]
["204934_s_at","HPN","This gene encodes a type II transmembrane serine protease that may be involved in diverse cellular functions, including blood coagulation and the maintenance of cell morphology. Expression of the encoded protein is associated with the growth and progression of cancers, particularly prostate cancer. The protein is cleaved into a catalytic serine protease chain and a non-catalytic scavenger receptor cysteine-rich chain, which associate via a single disulfide bond. Alternative splicing results in multiple transcript variants. Diseases associated with HPN include prostate cancer. Among its related pathways are Viral carcinogenesis. GO annotations related to this gene include serine-type endopeptidase activity and serine-type peptidase activity.       1. Smirnov et. al. Global Gene Expression Profiling of Circulating Tumor Cells; 2. Tozlu et. al. Identification of novel genes that co-cluster with estrogen receptor alpha in breast tumor biopsy specimens, using a large-scale real-time reverse transcription-PCR approach",6.965]
["212908_at","DNAJC16","DNAJC16 (DnaJ (Hsp40) Homolog, Subfamily C, Member 16) is a Protein Coding gene. An important paralog of this gene is DNAJC18.      1. Xu et. al. Merging microarray data from separate breast cancer studies provides a robust prognostic test",6.89]
["204045_at","TCEAL1","This gene encodes a member of the transcription elongation factor A (SII)-like (TCEAL) gene family. Members of this family may function as nuclear phosphoproteins that modulate transcription in a promoter context-dependent manner. The encoded protein is similar to transcription elongation factor A/transcription factor SII and contains a zinc finger-like motif as well as a sequence related to the transcription factor SII Pol II-binding region. It may exert its effects via protein-protein interactions with other transcriptional regulators rather than via direct binding of DNA. Multiple family members are located on the X chromosome. Alternative splicing results in multiple transcript variants encoding a single isoform. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding. An important paralog of this gene is WBP5.     1. Abba et. al. Gene expression signature of estrogen receptor α status in breast cancer",6.87]
["203368_at","CRELD1","This gene encodes a member of a subfamily of epidermal growth factor-related proteins. The encoded protein is characterized by a cysteine-rich with epidermal growth factor-like domain. This protein may function as a cell adhesion molecule. Mutations in this gene are the cause of atrioventricular septal defect. Alternate splicing results in multiple transcript variants. Diseases associated with CRELD1 include atrioventricular septal defect 2 and complete atrioventricular canal - fallot tetralogy. GO annotations related to this gene include calcium ion binding.     1. Dehan et. al. Chromosomal aberrations and gene expression profiles in non-small cell lung cancer",6.838]
["208628_s_at","YBX1","YBX1 (Y Box Binding Protein 1) is a Protein Coding gene. Diseases associated with YBX1 include liposarcoma and breast cancer. Among its related pathways are Signaling events mediated by PTP1B and Translational Control. GO annotations related to this gene include nucleic acid binding and transcription factor activity, sequence-specific DNA binding. An important paralog of this gene is YBX2.       1. Stratford, Anna L., et al. \"Y-box binding protein-1 serine 102 is a downstream target of p90 ribosomal S6 kinase in basal-like breast cancer cells.\" Breast Cancer Res 10.6 (2008): R99.",-6.805]
["218437_s_at","LZTFL1","This gene encodes a ubiquitously expressed protein that localizes to the cytoplasm. This protein interacts with Bardet-Biedl Syndrome (BBS) proteins and, through its interaction with BBS protein complexes, regulates protein trafficking to the ciliary membrane. Nonsense mutations in this gene cause a form of Bardet-Biedl Syndrome; a ciliopathy characterized in part by polydactyly, obesity, cognitive impairment, hypogonadism, and kidney failure. This gene may also function as a tumor suppressor; possibly by interacting with E-cadherin and the actin cytoskeleton and thereby regulating the transition of epithelial cells to mesenchymal cells. Alternative splicing of this gene results in multiple transcript variants. Diseases associated with LZTFL1 include bardet-biedl syndrome 17 and lztfl1- related bardet-biedl syndrome. Among its related pathways are Organelle biogenesis and maintenance and Cargo trafficking to the periciliary membrane. GO annotations related to this gene include identical protein binding and protein complex binding.     1. Chanrion et. al. A Gene Expression Signature that Can Predict the Recurrence of Tamoxifen-Treated Primary Breast Cancer",6.773]
["202870_s_at","CDC20","CDC20 appears to act as a regulatory protein interacting with several other proteins at multiple points in the cell cycle. It is required for two microtubule-dependent processes, nuclear movement prior to anaphase and chromosome separation.   1.Ein-Dor et. al. Outcome signature genes in breast cancer: is there a unique set? 2.Frasor et. al. Profiling of Estrogen Up- and Down-Regulated Gene Expression in Human Breast Cancer Cells: Insights into Gene Networks and Pathways Underlying Estrogenic Control of Proliferation and Cell Phenotype",-6.719]
["200934_at","DEK","This gene encodes a protein with one SAP domain. This protein binds to cruciform and superhelical DNA and induces positive supercoils into closed circular DNA, and is also involved in splice site selection during mRNA processing. Chromosomal aberrations involving this region, increased expression of this gene, and the presence of antibodies against this protein are all associated with various diseases. Two transcript variants encoding different isoforms have been found for this gene.     1.Bergamaschi et. al. Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer",-6.677]
["202095_s_at","BIRC5","This gene is a member of the inhibitor of apoptosis (IAP) gene family, which encode negative regulatory proteins that prevent apoptotic cell death. IAP family members usually contain multiple baculovirus IAP repeat (BIR) domains, but this gene encodes proteins with only a single BIR domain. The encoded proteins also lack a C-terminus RING finger domain. Gene expression is high during fetal development and in most tumors, yet low in adult tissues. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. Diseases associated with BIRC5 include childhood malignant schwannoma and cervical carcinosarcoma. Among its related pathways are Signaling by GPCR and Pathways in cancer.    1. Paik et. al. Gene Expression and Benefit of Chemotherapy in Women With Node-Negative, Estrogen Receptor–Positive Breast Cancer; 2. Sotiriou et. al. Gene Expression Profiling in Breast Cancer: Understanding the Molecular Basis of Histologic Grade To Improve Prognosis",-6.67]
["213911_s_at","H2AFZ","Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Nucleosomes consist of approximately 146 bp of DNA wrapped around a histone octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. This gene encodes a replication-independent member of the histone H2A family that is distinct from other members of the family. Studies in mice have shown that this particular histone is required for embryonic development and indicate that lack of functional histone H2A leads to embryonic lethality.     1.Kreike et. al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas",-6.651]
["201977_s_at","KIAA0141","It is also known as death ligand signal enhancer. Essential for the induction of death receptor-mediated apoptosis through the regulation of caspase activation.        1. Bai et. al. Analysis of gene expression patterns of ovarian cancer cell lines with different metastatic potentials; 2. Wang et al. Identification of Gene Expression Profiling in Hepatocellular Carcinoma Using cDNA Microarrays",6.61]
["210958_s_at","MAST4","This gene encodes a member of the microtubule-associated serine/threonine protein kinases. The proteins in this family contain a domain that gives the kinase the ability to determine its own scaffold to control the effects of their kinase activities. Alternative splicing results in multiple transcript variants encoding different isoforms. GO annotations related to this gene include transferase activity, transferring phosphorus-containing groups and protein tyrosine kinase activity. An important paralog of this gene is MAST3.        1. Woodfield et al. Identification of primary gene targets of TFAP2C in hormone responsive breast carcinoma cells",6.568]
["203418_at","CCNA2","The protein encoded by this gene belongs to the highly conserved cyclin family, whose members are characterized by a dramatic periodicity in protein abundance through the cell cycle. Cyclins function as regulators of CDK kinases. Different cyclins exhibit distinct expression and degradation patterns which contribute to the temporal coordination of each mitotic event. In contrast to cyclin A1, which is present only in germ cells, this cyclin is expressed in all tissues tested. This cyclin binds and activates CDC2 or CDK2 kinases, and thus promotes both cell cycle G1/S and G2/M transitions. Diseases associated with CCNA2 include thyroid lymphoma and retinoblastoma. Among its related pathways are GPCR Pathway and Nanog in Mammalian ESC Pluripotency. GO annotations related to this gene include protein kinase binding. An important paralog of this gene is CCND2.        1. Sotiriou et. al. Gene Expression Profiling in Breast Cancer: Understanding the Molecular Basis of Histologic Grade To Improve Prognosis; 2. Lehmann et. al. Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies",-6.55]
["57540_at","RBKS","This gene encodes a member of the carbohydrate kinase PfkB family. The encoded protein phosphorylates ribose to form ribose-5-phosphate in the presence of ATP and magnesium as a first step in ribose metabolism. Alternative splicing results in multiple transcript variants. Among its related pathways are Pentose phosphate pathway. GO annotations related to this gene include ribokinase activity.       1. Gonzalez-Malerva et. al. High-throughput ectopic expression screen for tamoxifen resistance identifies an atypical kinase that blocks autophagy",6.549]
["214077_x_at","MEIS3P1","This gene appears to be a retrotransposed pseudogene based on its lack of exons compared to other family members, one of which is found on chromosome 19 (MEIS3). It does appear to be transcribed and has an ORF that may encode a protein of similar size and sequence to that encoded by MEIS3. It may not be very biologically meaningful.",6.532]
["214039_s_at","LAPTM4B","Increased expression of LAPTM4B has been found in breast, liver, lung, ovarian, uterine, gastric cancers. Elevated LAPTM4B level contributes to chemotherapy resistance in breast cancer. It was found that overexpression of LAPTM4B causes anthracyclines (doxorubicin, daunorubicin, and epirubicin) resistance by retaining drug in the cytoplasm and decreasing nuclear localization of drug and drug induced DNA damage.      1.Li et. al. Amplification of LAPTM4B and YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer",-6.516]
["205141_at","ANG","The protein encoded by this gene is an exceedingly potent mediator of new blood vessel formation. It hydrolyzes cellular tRNAs resulting in decreased protein synthesis and is similar to pancreatic ribonuclease. In addition, the mature peptide has antimicrobial activity against some bacteria and fungi, including S. pneumoniae and C. albicans. Alternative splicing results in two transcript variants encoding the same protein. This gene and the gene that encodes ribonuclease, RNase A family, 4 share promoters and 5' exons. Each gene splices to a unique downstream exon that contains its complete coding region. Diseases associated with ANG include ang-related amyotrophic lateral sclerosis and amyotrophic lateral sclerosis 9. Among its related pathways are Cell junction organization. GO annotations related to this gene include protein homodimerization activity and actin binding. An important paralog of this gene is RNASE1. Not much literature found.",6.471]
["209625_at","PIGH","This gene encodes an endoplasmic reticulum associated protein that is involved in glycosylphosphatidylinositol (GPI)-anchor biosynthesis. The GPI anchor is a glycolipid found on many blood cells and which serves to anchor proteins to the cell surface. The protein encoded by this gene is a subunit of the GPI N-acetylglucosaminyl (GlcNAc) transferase that transfers GlcNAc to phosphatidylinositol (PI) on the cytoplasmic side of the endoplasmic reticulum. Among its related pathways are Transport to the Golgi and subsequent modification and Metabolism. GO annotations related to this gene include phosphatidylinositol N-acetylglucosaminyltransferase activity. Not much literature found.",6.471]
["202107_s_at","MCM2","The protein encoded by this gene is one of the highly conserved mini-chromosome maintenance proteins (MCM) that are involved in the initiation of eukaryotic genome replication. The hexameric protein complex formed by MCM proteins is a key component of the pre-replication complex (pre_RC) and may be involved in the formation of replication forks and in the recruitment of other DNA replication related proteins. This protein forms a complex with MCM4, 6, and 7, and has been shown to regulate the helicase activity of the complex. This protein is phosphorylated, and thus regulated by, protein kinases CDC2 and CDC7.    1. Perou et. al. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers; 2. Sotiriou et. al. Breast cancer classification and prognosis based on gene expression profiles from a population-based study",-6.47]
["40016_g_at","MAST4","Same as previous",6.458]
["208767_s_at","LAPTM4B","Same as previous",-6.422]

{"sheet":"Top30_Quantile","index":2,"n_rows":31,"n_cols":4,"rows_kept":31,"cut":false,"hidden":false,"merged":[]}
["Probe set name","Gene symbol","Annotation","t-statistic"]
["204703_at","IFT88","This gene encodes a member of the tetratrico peptide repeat (TPR) family. Mutations of a similar gene in mouse can cause polycystic kidney disease. Two transcript variants encoding distinct isoforms have been identified for this gene. Diseases associated with IFT88 include orofaciodigital syndrome i and polycystic kidney disease. Among its related pathways are Signaling by GPCR and Organelle biogenesis and maintenance. GO annotations related to this gene include kinesin binding.    1. Kuehn et. al. von Hippel-Lindau: A Tumor Suppressor Links Microtubules to Ciliogenesis and Cancer Development",8.667]
["205441_at","OCEL1","Not much information available about this gene (surprising!)     1. Neilsen et. Al. Mutant p53 uses p63 as a molecular chaperone to alter gene expression and induce a pro-invasive secretome",8.433]
["201930_at","MCM6","MCM6 is one of the highly conserved mini-chromosome maintenance proteins (MCM) that are essential for the initiation of eukaryotic genome replication.   Link to breast cancer: 1. Van't Veer, Laura J., et al. \"Gene expression profiling predicts clinical outcome of breast cancer.\" nature 415.6871 (2002): 530-536. 2. Sotiriou, Christos, et al. \"Breast cancer classification and prognosis based on gene expression profiles from a population-based study.\" Proceedings of the National Academy of Sciences 100.18 (2003): 10393-10398.",-7.89]
["208628_s_at","YBX1","YBX1 (Y Box Binding Protein 1) is a Protein Coding gene. Diseases associated with YBX1 include liposarcoma and breast cancer. Among its related pathways are Signaling events mediated by PTP1B and Translational Control. GO annotations related to this gene include nucleic acid binding and transcription factor activity, sequence-specific DNA binding. An important paralog of this gene is YBX2.       1. Stratford, Anna L., et al. \"Y-box binding protein-1 serine 102 is a downstream target of p90 ribosomal S6 kinase in basal-like breast cancer cells.\" Breast Cancer Res 10.6 (2008): R99.",-7.879]
["212736_at","C16orf45","This gene has 11 transcripts (splice variants), 1 gene allele, 62 orthologues, is a member of 1 Ensembl protein family and is associated with 5 phenotypes. C16orf45 (Chromosome 16 Open Reading Frame 45) is a Protein Coding gene. Not much literature available.   1.Partheen et. al. Expression analysis of stage III serous ovarian adenocarcinoma distinguishes a sub-group of survivors. This is the only one I can find somewhat related (ovarian is unique for women)",7.331]
["206197_at","NME5","NME5 (NME/NM23 Family Member 5) is a Protein Coding gene. Among its related pathways are Carbon metabolism and Metabolism. GO annotations related to this gene include nucleoside diphosphate kinase activity. An important paralog of this gene is NME7. Does not seem to have NDK kinase activity. Confers protection from cell death by Bax and alters the cellular levels of several antioxidant enzymes including Gpx5. May play a role in spermiogenesis by increasing the ability of late-stage spermatids to eliminate reactive oxygen species (By similarity).     1. Parris et. al. Clinical Implications of Gene Dosage and Gene Expression Patterns in Diploid Breast Carcinoma",7.175]
["218692_at","SYBU","Syntabulin/GOLSYN is part of a kinesin motor-adaptor complex that is critical for the anterograde axonal transport of active zone components and contributes to activity-dependent presynaptic assembly during neuronal development. SYBU (Syntabulin (Syntaxin-Interacting)) is a Protein Coding gene. GO annotations related to this gene include microtubule binding and syntaxin-1 binding. An important paralog of this gene is SNPH.     1.Casa et. al. Estrogen and insulin-like growth factor-I (IGF-I) independently down-regulate critical repressors of breast cancer growth (29 cited, not many frequently cited papers)",7.16]
["213911_s_at","H2AFZ","Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Nucleosomes consist of approximately 146 bp of DNA wrapped around a histone octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. This gene encodes a replication-independent member of the histone H2A family that is distinct from other members of the family. Studies in mice have shown that this particular histone is required for embryonic development and indicate that lack of functional histone H2A leads to embryonic lethality.     1.Kreike et. al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas",-7.111]
["204063_s_at","ULK2","This gene encodes a protein that is similar to a serine/threonine kinase in C. elegans which is involved in axonal elongation. The structure of this protein is similar to the C. elegans protein in that both proteins have an N-terminal kinase domain, a central proline/serine rich (PS) domain, and a C-terminal (C) domain. The gene is located within the Smith-Magenis syndrome region on chromosome 17. Alternatively spliced transcript variants encoding the same protein have been identified. Among its related pathways are mTOR signalling and Translation Insulin regulation of translation. GO annotations related to this gene include transferase activity, transferring phosphorus-containing groups and protein tyrosine kinase activity. An important paralog of this gene is ULK3.      1. Ouyang et. al. MicroRNA Profiling Implies New Markers of Chemoresistance of Triple-Negative Breast Cancer; 2. Sabine et. al. Gene expression profiling of response to mTOR inhibitor everolimus in pre-operatively treated post-menopausal women with oestrogen receptor-positive breast cancer",7.072]
["208627_s_at","YBX1","Same as previous",-7.008]
["204962_s_at","CENPA","Centromeres are the differentiated chromosomal domains that specify the mitotic behavior of chromosomes. This gene encodes a centromere protein which contains a histone H3 related histone fold domain that is required for targeting to the centromere. Centromere protein A is proposed to be a component of a modified nucleosome or nucleosome-like structure in which it replaces 1 or both copies of conventional histone H3 in the (H3-H4)2 tetrameric core of the nucleosome particle. The protein is a replication-independent histone that is a member of the histone H3 family. Alternative splicing results in multiple transcript variants encoding distinct isoforms.         1.Sotiriou et. al. Gene Expression Profiling in Breast Cancer: Understanding the Molecular Basis of Histologic Grade To Improve Prognosis; 2. Ma et. al. Gene expression profiles of human breast cancer progression",-6.994]
["203143_s_at","KIAA0040","Not much description about this gene      1. Peng et. al. Tumor-Associated Galectin-3 Modulates the Function of Tumor-Reactive T Cells; 2. Jenssen et. al. Associations between gene expressions in breast cancer and patient survival",6.956]
["212908_at","DNAJC16","DNAJC16 (DnaJ (Hsp40) Homolog, Subfamily C, Member 16) is a Protein Coding gene. An important paralog of this gene is DNAJC18.      1. Xu et. al. Merging microarray data from separate breast cancer studies provides a robust prognostic test",6.876]
["204934_s_at","HPN","This gene encodes a type II transmembrane serine protease that may be involved in diverse cellular functions, including blood coagulation and the maintenance of cell morphology. Expression of the encoded protein is associated with the growth and progression of cancers, particularly prostate cancer. The protein is cleaved into a catalytic serine protease chain and a non-catalytic scavenger receptor cysteine-rich chain, which associate via a single disulfide bond. Alternative splicing results in multiple transcript variants. Diseases associated with HPN include prostate cancer. Among its related pathways are Viral carcinogenesis. GO annotations related to this gene include serine-type endopeptidase activity and serine-type peptidase activity.       1. Smirnov et. al. Global Gene Expression Profiling of Circulating Tumor Cells; 2. Tozlu et. al. Identification of novel genes that co-cluster with estrogen receptor alpha in breast tumor biopsy specimens, using a large-scale real-time reverse transcription-PCR approach",6.846]
["204045_at","TCEAL1","This gene encodes a member of the transcription elongation factor A (SII)-like (TCEAL) gene family. Members of this family may function as nuclear phosphoproteins that modulate transcription in a promoter context-dependent manner. The encoded protein is similar to transcription elongation factor A/transcription factor SII and contains a zinc finger-like motif as well as a sequence related to the transcription factor SII Pol II-binding region. It may exert its effects via protein-protein interactions with other transcriptional regulators rather than via direct binding of DNA. Multiple family members are located on the X chromosome. Alternative splicing results in multiple transcript variants encoding a single isoform. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding. An important paralog of this gene is WBP5.     1. Abba et. al. Gene expression signature of estrogen receptor α status in breast cancer",6.816]
["203368_at","CRELD1","This gene encodes a member of a subfamily of epidermal growth factor-related proteins. The encoded protein is characterized by a cysteine-rich with epidermal growth factor-like domain. This protein may function as a cell adhesion molecule. Mutations in this gene are the cause of atrioventricular septal defect. Alternate splicing results in multiple transcript variants. Diseases associated with CRELD1 include atrioventricular septal defect 2 and complete atrioventricular canal - fallot tetralogy. GO annotations related to this gene include calcium ion binding.     1. Dehan et. al. Chromosomal aberrations and gene expression profiles in non-small cell lung cancer",6.728]
["203418_at","CCNA2","The protein encoded by this gene belongs to the highly conserved cyclin family, whose members are characterized by a dramatic periodicity in protein abundance through the cell cycle. Cyclins function as regulators of CDK kinases. Different cyclins exhibit distinct expression and degradation patterns which contribute to the temporal coordination of each mitotic event. In contrast to cyclin A1, which is present only in germ cells, this cyclin is expressed in all tissues tested. This cyclin binds and activates CDC2 or CDK2 kinases, and thus promotes both cell cycle G1/S and G2/M transitions. Diseases associated with CCNA2 include thyroid lymphoma and retinoblastoma. Among its related pathways are GPCR Pathway and Nanog in Mammalian ESC Pluripotency. GO annotations related to this gene include protein kinase binding. An important paralog of this gene is CCND2.        1. Sotiriou et. al. Gene Expression Profiling in Breast Cancer: Understanding the Molecular Basis of Histologic Grade To Improve Prognosis; 2. Lehmann et. al. Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies",-6.725]
["214039_s_at","LAPTM4B","Increased expression of LAPTM4B has been found in breast, liver, lung, ovarian, uterine, gastric cancers. Elevated LAPTM4B level contributes to chemotherapy resistance in breast cancer. It was found that overexpression of LAPTM4B causes anthracyclines (doxorubicin, daunorubicin, and epirubicin) resistance by retaining drug in the cytoplasm and decreasing nuclear localization of drug and drug induced DNA damage.      1.Li et. al. Amplification of LAPTM4B and YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer",-6.721]
["203358_s_at","EZH2","This gene encodes a member of the Polycomb-group (PcG) family. PcG family members form multimeric protein complexes, which are involved in maintaining the transcriptional repressive state of genes over successive cell generations. This protein associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. This protein may play a role in the hematopoietic and central nervous systems. Multiple alternatively splcied transcript variants encoding distinct isoforms have been identified for this gene. Diseases associated with EZH2 include periodic fever, aphthous stomatitis, pharyngitis and adenitis and weaver syndrome.  1. Kleer et. al. EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells",-6.719]
["202870_s_at","CDC20","CDC20 appears to act as a regulatory protein interacting with several other proteins at multiple points in the cell cycle. It is required for two microtubule-dependent processes, nuclear movement prior to anaphase and chromosome separation.   1.Ein-Dor et. al. Outcome signature genes in breast cancer: is there a unique set? 2.Frasor et. al. Profiling of Estrogen Up- and Down-Regulated Gene Expression in Human Breast Cancer Cells: Insights into Gene Networks and Pathways Underlying Estrogenic Control of Proliferation and Cell Phenotype",-6.708]
["202095_s_at","BIRC5","This gene is a member of the inhibitor of apoptosis (IAP) gene family, which encode negative regulatory proteins that prevent apoptotic cell death. IAP family members usually contain multiple baculovirus IAP repeat (BIR) domains, but this gene encodes proteins with only a single BIR domain. The encoded proteins also lack a C-terminus RING finger domain. Gene expression is high during fetal development and in most tumors, yet low in adult tissues. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. Diseases associated with BIRC5 include childhood malignant schwannoma and cervical carcinosarcoma. Among its related pathways are Signaling by GPCR and Pathways in cancer.    1. Paik et. al. Gene Expression and Benefit of Chemotherapy in Women With Node-Negative, Estrogen Receptor–Positive Breast Cancer; 2. Sotiriou et. al. Gene Expression Profiling in Breast Cancer: Understanding the Molecular Basis of Histologic Grade To Improve Prognosis",-6.687]
["200934_at","DEK","This gene encodes a protein with one SAP domain. This protein binds to cruciform and superhelical DNA and induces positive supercoils into closed circular DNA, and is also involved in splice site selection during mRNA processing. Chromosomal aberrations involving this region, increased expression of this gene, and the presence of antibodies against this protein are all associated with various diseases. Two transcript variants encoding different isoforms have been found for this gene.     1.Bergamaschi et. al. Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer",-6.677]
["203801_at","MRPS14","Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a 28S subunit protein that belongs to the ribosomal protein S14P family. Alternative splicing results in multiple transcript variants. Among its related pathways are Organelle biogenesis and maintenance and Viral mRNA Translation. GO annotations related to this gene include poly(A) RNA binding and structural constituent of ribosome.         1. Neo et. al. Identification of discriminators of hepatoma by gene expression profiling using a minimal dataset approach; 2. Ching et. al. Integrated analysis of copy number and loss of heterozygosity in primary breast carcinomas using high-density SNP array",6.653]
["218437_s_at","LZTFL1","This gene encodes a ubiquitously expressed protein that localizes to the cytoplasm. This protein interacts with Bardet-Biedl Syndrome (BBS) proteins and, through its interaction with BBS protein complexes, regulates protein trafficking to the ciliary membrane. Nonsense mutations in this gene cause a form of Bardet-Biedl Syndrome; a ciliopathy characterized in part by polydactyly, obesity, cognitive impairment, hypogonadism, and kidney failure. This gene may also function as a tumor suppressor; possibly by interacting with E-cadherin and the actin cytoskeleton and thereby regulating the transition of epithelial cells to mesenchymal cells. Alternative splicing of this gene results in multiple transcript variants. Diseases associated with LZTFL1 include bardet-biedl syndrome 17 and lztfl1- related bardet-biedl syndrome. Among its related pathways are Organelle biogenesis and maintenance and Cargo trafficking to the periciliary membrane. GO annotations related to this gene include identical protein binding and protein complex binding.     1. Chanrion et. al. A Gene Expression Signature that Can Predict the Recurrence of Tamoxifen-Treated Primary Breast Cancer",6.633]
["212320_at","TUBB","This gene encodes a beta tubulin protein. This protein forms a dimer with alpha tubulin and acts as a structural component of microtubules. Mutations in this gene cause cortical dysplasia, complex, with other brain malformations 6. Alternative splicing results in multiple splice variants. There are multiple pseudogenes for this gene on chromosomes 1, 6, 7, 8, 9, and 13. Diseases associated with TUBB include cortical dysplasia, complex, with other brain malformations 6 and hereditary cerebral amyloid angiopathy. Among its related pathways are GPCR Pathway and PAK Pathway. GO annotations related to this gene include GTP binding and structural molecule activity. An important paralog of this gene is TUBB3.      1. Gianni et. al. Gene Expression Profiles in Paraffin-Embedded Core Biopsy Tissue Predict Response to Chemotherapy in Women With Locally Advanced Breast Cancer; 2. Honma et. al. RPN2 gene confers docetaxel resistance in breast cancer",-6.599]
["208767_s_at","LAPTM4B","Same as previous",-6.552]
["202107_s_at","MCM2","The protein encoded by this gene is one of the highly conserved mini-chromosome maintenance proteins (MCM) that are involved in the initiation of eukaryotic genome replication. The hexameric protein complex formed by MCM proteins is a key component of the pre-replication complex (pre_RC) and may be involved in the formation of replication forks and in the recruitment of other DNA replication related proteins. This protein forms a complex with MCM4, 6, and 7, and has been shown to regulate the helicase activity of the complex. This protein is phosphorylated, and thus regulated by, protein kinases CDC2 and CDC7.    1. Perou et. al. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers; 2. Sotiriou et. al. Breast cancer classification and prognosis based on gene expression profiles from a population-based study",-6.542]
["214077_x_at","MEIS3P1","This gene appears to be a retrotransposed pseudogene based on its lack of exons compared to other family members, one of which is found on chromosome 19 (MEIS3). It does appear to be transcribed and has an ORF that may encode a protein of similar size and sequence to that encoded by MEIS3. It may not be very biologically meaningful.",6.526]
["201977_s_at","KIAA0141","It is also known as death ligand signal enhancer. Essential for the induction of death receptor-mediated apoptosis through the regulation of caspase activation.        1. Bai et. al. Analysis of gene expression patterns of ovarian cancer cell lines with different metastatic potentials; 2. Wang et al. Identification of Gene Expression Profiling in Hepatocellular Carcinoma Using cDNA Microarrays",6.525]
["210958_s_at","MAST4","This gene encodes a member of the microtubule-associated serine/threonine protein kinases. The proteins in this family contain a domain that gives the kinase the ability to determine its own scaffold to control the effects of their kinase activities. Alternative splicing results in multiple transcript variants encoding different isoforms. GO annotations related to this gene include transferase activity, transferring phosphorus-containing groups and protein tyrosine kinase activity. An important paralog of this gene is MAST3.        1. Woodfield et al. Identification of primary gene targets of TFAP2C in hormone responsive breast carcinoma cells",6.523]

{"sheet":"Top30_Cyclicloess","index":3,"n_rows":31,"n_cols":4,"rows_kept":31,"cut":false,"hidden":false,"merged":[]}
["Probe set name","Gene symbol","Annotation","t-statistic"]
["205441_at","OCEL1","Not much information available about this gene (surprising!)     1. Neilsen et. Al. Mutant p53 uses p63 as a molecular chaperone to alter gene expression and induce a pro-invasive secretome",8.49830828285472]
["204703_at","IFT88","This gene encodes a member of the tetratrico peptide repeat (TPR) family. Mutations of a similar gene in mouse can cause polycystic kidney disease. Two transcript variants encoding distinct isoforms have been identified for this gene. Diseases associated with IFT88 include orofaciodigital syndrome i and polycystic kidney disease. Among its related pathways are Signaling by GPCR and Organelle biogenesis and maintenance. GO annotations related to this gene include kinesin binding.    1. Kuehn et. al. von Hippel-Lindau: A Tumor Suppressor Links Microtubules to Ciliogenesis and Cancer Development",8.34472746678113]
["201930_at","MCM6","MCM6 is one of the highly conserved mini-chromosome maintenance proteins (MCM) that are essential for the initiation of eukaryotic genome replication.   Link to breast cancer: 1. Van't Veer, Laura J., et al. \"Gene expression profiling predicts clinical outcome of breast cancer.\" nature 415.6871 (2002): 530-536. 2. Sotiriou, Christos, et al. \"Breast cancer classification and prognosis based on gene expression profiles from a population-based study.\" Proceedings of the National Academy of Sciences 100.18 (2003): 10393-10398.",-8.03997588256659]
["208628_s_at","YBX1","YBX1 (Y Box Binding Protein 1) is a Protein Coding gene. Diseases associated with YBX1 include liposarcoma and breast cancer. Among its related pathways are Signaling events mediated by PTP1B and Translational Control. GO annotations related to this gene include nucleic acid binding and transcription factor activity, sequence-specific DNA binding. An important paralog of this gene is YBX2.       1. Stratford, Anna L., et al. \"Y-box binding protein-1 serine 102 is a downstream target of p90 ribosomal S6 kinase in basal-like breast cancer cells.\" Breast Cancer Res 10.6 (2008): R99.",-7.87167971865425]
["213911_s_at","H2AFZ","Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Nucleosomes consist of approximately 146 bp of DNA wrapped around a histone octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. This gene encodes a replication-independent member of the histone H2A family that is distinct from other members of the family. Studies in mice have shown that this particular histone is required for embryonic development and indicate that lack of functional histone H2A leads to embryonic lethality.     1.Kreike et. al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas",-7.38538951217912]
["206197_at","NME5","NME5 (NME/NM23 Family Member 5) is a Protein Coding gene. Among its related pathways are Carbon metabolism and Metabolism. GO annotations related to this gene include nucleoside diphosphate kinase activity. An important paralog of this gene is NME7. Does not seem to have NDK kinase activity. Confers protection from cell death by Bax and alters the cellular levels of several antioxidant enzymes including Gpx5. May play a role in spermiogenesis by increasing the ability of late-stage spermatids to eliminate reactive oxygen species (By similarity).     1. Parris et. al. Clinical Implications of Gene Dosage and Gene Expression Patterns in Diploid Breast Carcinoma",-7.14049196074817]
["204962_s_at","CENPA","Centromeres are the differentiated chromosomal domains that specify the mitotic behavior of chromosomes. This gene encodes a centromere protein which contains a histone H3 related histone fold domain that is required for targeting to the centromere. Centromere protein A is proposed to be a component of a modified nucleosome or nucleosome-like structure in which it replaces 1 or both copies of conventional histone H3 in the (H3-H4)2 tetrameric core of the nucleosome particle. The protein is a replication-independent histone that is a member of the histone H3 family. Alternative splicing results in multiple transcript variants encoding distinct isoforms.         1.Sotiriou et. al. Gene Expression Profiling in Breast Cancer: Understanding the Molecular Basis of Histologic Grade To Improve Prognosis; 2. Ma et. al. Gene expression profiles of human breast cancer progression",-7.02731522143091]
["212736_at","C16orf45","This gene has 11 transcripts (splice variants), 1 gene allele, 62 orthologues, is a member of 1 Ensembl protein family and is associated with 5 phenotypes. C16orf45 (Chromosome 16 Open Reading Frame 45) is a Protein Coding gene. Not much literature available.   1.Partheen et. al. Expression analysis of stage III serous ovarian adenocarcinoma distinguishes a sub-group of survivors. This is the only one I can find somewhat related (ovarian is unique for women)",6.99114163860868]
["204934_s_at","HPN","This gene encodes a type II transmembrane serine protease that may be involved in diverse cellular functions, including blood coagulation and the maintenance of cell morphology. Expression of the encoded protein is associated with the growth and progression of cancers, particularly prostate cancer. The protein is cleaved into a catalytic serine protease chain and a non-catalytic scavenger receptor cysteine-rich chain, which associate via a single disulfide bond. Alternative splicing results in multiple transcript variants. Diseases associated with HPN include prostate cancer. Among its related pathways are Viral carcinogenesis. GO annotations related to this gene include serine-type endopeptidase activity and serine-type peptidase activity.       1. Smirnov et. al. Global Gene Expression Profiling of Circulating Tumor Cells; 2. Tozlu et. al. Identification of novel genes that co-cluster with estrogen receptor alpha in breast tumor biopsy specimens, using a large-scale real-time reverse transcription-PCR approach",6.93822426193036]
["203418_at","CCNA2","The protein encoded by this gene belongs to the highly conserved cyclin family, whose members are characterized by a dramatic periodicity in protein abundance through the cell cycle. Cyclins function as regulators of CDK kinases. Different cyclins exhibit distinct expression and degradation patterns which contribute to the temporal coordination of each mitotic event. In contrast to cyclin A1, which is present only in germ cells, this cyclin is expressed in all tissues tested. This cyclin binds and activates CDC2 or CDK2 kinases, and thus promotes both cell cycle G1/S and G2/M transitions. Diseases associated with CCNA2 include thyroid lymphoma and retinoblastoma. Among its related pathways are GPCR Pathway and Nanog in Mammalian ESC Pluripotency. GO annotations related to this gene include protein kinase binding. An important paralog of this gene is CCND2.        1. Sotiriou et. al. Gene Expression Profiling in Breast Cancer: Understanding the Molecular Basis of Histologic Grade To Improve Prognosis; 2. Lehmann et. al. Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies",-6.92102857440418]
["200996_at","ACTR3","The specific function of this gene has not yet been determined; however, the protein it encodes is known to be a major constituent of the ARP2/3 complex. This complex is located at the cell surface and is essential to cell shape and motility through lamellipodial actin assembly and protrusion. Three transcript variants encoding two different isoforms have been found for this gene. Diseases associated with ACTR3 include wiskott-aldrich syndrome. Among its related pathways are Immune System and Signaling by GPCR.   1. Siripurapu et. al. DBC2 Significantly Influences Cell-cycle, Apoptosis, Cytoskeleton and Membrane-trafficking Pathways",6.87507941715861]
["202095_s_at","BIRC5","This gene is a member of the inhibitor of apoptosis (IAP) gene family, which encode negative regulatory proteins that prevent apoptotic cell death. IAP family members usually contain multiple baculovirus IAP repeat (BIR) domains, but this gene encodes proteins with only a single BIR domain. The encoded proteins also lack a C-terminus RING finger domain. Gene expression is high during fetal development and in most tumors, yet low in adult tissues. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. Diseases associated with BIRC5 include childhood malignant schwannoma and cervical carcinosarcoma. Among its related pathways are Signaling by GPCR and Pathways in cancer.    1. Paik et. al. Gene Expression and Benefit of Chemotherapy in Women With Node-Negative, Estrogen Receptor–Positive Breast Cancer; 2. Sotiriou et. al. Gene Expression Profiling in Breast Cancer: Understanding the Molecular Basis of Histologic Grade To Improve Prognosis",-6.83889051405831]
["203143_s_at","KIAA0040","KIAA0040 (KIAA0040) is a Protein Coding gene. Not much information.        1. Jenssen et. al. Associations between gene expressions in breast cancer and patient survival",6.79896656878522]
["212789_at","NCAPD3","NCAPD3 (Non-SMC Condensin II Complex Subunit D3) is a Protein Coding gene. Among its related pathways are Mitotic Prophase and Cell cycle_Chromosome condensation in prometaphase. GO annotations related to this gene include binding and methylated histone binding.           1.  Bandhakavi et. al. Quantitative nuclear proteomics identifies mTOR regulation of DNA damage response",6.79515882511658]
["212908_at","DNAJC16","DNAJC16 (DnaJ (Hsp40) Homolog, Subfamily C, Member 16) is a Protein Coding gene. An important paralog of this gene is DNAJC18.      1. Xu et. al. Merging microarray data from separate breast cancer studies provides a robust prognostic test",-6.77349598527638]
["218692_at","SYBU","Syntabulin/GOLSYN is part of a kinesin motor-adaptor complex that is critical for the anterograde axonal transport of active zone components and contributes to activity-dependent presynaptic assembly during neuronal development. SYBU (Syntabulin (Syntaxin-Interacting)) is a Protein Coding gene. GO annotations related to this gene include microtubule binding and syntaxin-1 binding. An important paralog of this gene is SNPH.     1.Casa et. al. Estrogen and insulin-like growth factor-I (IGF-I) independently down-regulate critical repressors of breast cancer growth (29 cited, not many frequently cited papers)",-6.77067408321252]
["212021_s_at","MKI67","This gene encodes a nuclear protein that is associated with and may be necessary for cellular proliferation. Alternatively spliced transcript variants have been described. A related pseudogene exists on chromosome X. MKI67 (Marker Of Proliferation Ki-67) is a Protein Coding gene. Diseases associated with MKI67 include Pancreatic Neuroendocrine Tumor and Uterus Leiomyosarcoma. Among its related pathways are Neuroscience and DNA Damage. GO annotations related to this gene include poly(A) RNA binding and protein C-terminus binding.          1. Hou et. al. MicroRNA-519d targets MKi67 and suppresses cell growth in the hepatocellular carcinoma cell line QGY-7703; 2. Gyorffy et. al. An online survival analysis tool to rapidly assess the effect of 22,277 genes on breast cancer prognosis using microarray data of 1,809 patients",6.75053341837562]
["204045_at","TCEAL1","This gene encodes a member of the transcription elongation factor A (SII)-like (TCEAL) gene family. Members of this family may function as nuclear phosphoproteins that modulate transcription in a promoter context-dependent manner. The encoded protein is similar to transcription elongation factor A/transcription factor SII and contains a zinc finger-like motif as well as a sequence related to the transcription factor SII Pol II-binding region. It may exert its effects via protein-protein interactions with other transcriptional regulators rather than via direct binding of DNA. Multiple family members are located on the X chromosome. Alternative splicing results in multiple transcript variants encoding a single isoform. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding. An important paralog of this gene is WBP5.     1. Abba et. al. Gene expression signature of estrogen receptor α status in breast cancer",-6.72198798072894]
["202705_at","CCNB2","Cyclin B2 is a member of the cyclin family, specifically the B-type cyclins. The B-type cyclins, B1 and B2, associate with p34cdc2 and are essential components of the cell cycle regulatory machinery. B1 and B2 differ in their subcellular localization. Cyclin B1 co-localizes with microtubules, whereas cyclin B2 is primarily associated with the Golgi region. Cyclin B2 also binds to transforming growth factor beta RII and thus cyclin B2/cdc2 may play a key role in transforming growth factor beta-mediated cell cycle control. Diseases associated with CCNB2 include anauxetic dysplasia and breast cancer. Among its related pathways are GPCR Pathway and Regulation of PLK1 Activity at G2/M Transition. GO annotations related to this gene include protein kinase binding. An important paralog of this gene is CCND2.        1. Bertucci et. al. Gene Expression Profiling for Molecular Characterization of Inflammatory Breast Cancer and Prediction of Response to Chemotherapy; 2. Oh et. al. Estrogen-Regulated Genes Predict Survival in Hormone Receptor–Positive Breast Cancers",-6.69817528919177]
["202870_s_at","CDC20","CDC20 appears to act as a regulatory protein interacting with several other proteins at multiple points in the cell cycle. It is required for two microtubule-dependent processes, nuclear movement prior to anaphase and chromosome separation.   1.Ein-Dor et. al. Outcome signature genes in breast cancer: is there a unique set? 2.Frasor et. al. Profiling of Estrogen Up- and Down-Regulated Gene Expression in Human Breast Cancer Cells: Insights into Gene Networks and Pathways Underlying Estrogenic Control of Proliferation and Cell Phenotype",-6.69434874182276]
["204063_s_at","ULK2","This gene encodes a protein that is similar to a serine/threonine kinase in C. elegans which is involved in axonal elongation. The structure of this protein is similar to the C. elegans protein in that both proteins have an N-terminal kinase domain, a central proline/serine rich (PS) domain, and a C-terminal (C) domain. The gene is located within the Smith-Magenis syndrome region on chromosome 17. Alternatively spliced transcript variants encoding the same protein have been identified. Among its related pathways are mTOR signalling and Translation Insulin regulation of translation. GO annotations related to this gene include transferase activity, transferring phosphorus-containing groups and protein tyrosine kinase activity. An important paralog of this gene is ULK3.      1. Ouyang et. al. MicroRNA Profiling Implies New Markers of Chemoresistance of Triple-Negative Breast Cancer; 2. Sabine et. al. Gene expression profiling of response to mTOR inhibitor everolimus in pre-operatively treated post-menopausal women with oestrogen receptor-positive breast cancer",-6.68403789824709]
["210052_s_at","TPX2","TPX2 (TPX2, Microtubule Nucleation Factor) is a Protein Coding gene. Diseases associated with TPX2 include Hepatocellular Carcinoma. Among its related pathways are Regulation of TP53 Activity and PLK1 signaling events. GO annotations related to this gene include GTP binding and protein kinase binding.      1. Warner et. al. Validation of TPX2 as a potential therapeutic target in pancreatic cancer cells; 2. Chang et. al. The TPX2 gene is a promising diagnostic and therapeutic target for cervical cancer; 3. Wei et. al. TPX2 is a novel prognostic marker for the growth and metastasis of colon cancer",6.63123875525619]
["214039_s_at","LAPTM4B","Increased expression of LAPTM4B has been found in breast, liver, lung, ovarian, uterine, gastric cancers. Elevated LAPTM4B level contributes to chemotherapy resistance in breast cancer. It was found that overexpression of LAPTM4B causes anthracyclines (doxorubicin, daunorubicin, and epirubicin) resistance by retaining drug in the cytoplasm and decreasing nuclear localization of drug and drug induced DNA damage.      1.Li et. al. Amplification of LAPTM4B and YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer",6.62700195109225]
["203358_s_at","EZH2","This gene encodes a member of the Polycomb-group (PcG) family. PcG family members form multimeric protein complexes, which are involved in maintaining the transcriptional repressive state of genes over successive cell generations. This protein associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. This protein may play a role in the hematopoietic and central nervous systems. Multiple alternatively splcied transcript variants encoding distinct isoforms have been identified for this gene. Diseases associated with EZH2 include periodic fever, aphthous stomatitis, pharyngitis and adenitis and weaver syndrome.  1. Kleer et. al. EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells",-6.61348561282498]
["208627_s_at","YBX1","Same as previous",-6.6062272770589]
["210958_s_at","MAST4","This gene encodes a member of the microtubule-associated serine/threonine protein kinases. The proteins in this family contain a domain that gives the kinase the ability to determine its own scaffold to control the effects of their kinase activities. Alternative splicing results in multiple transcript variants encoding different isoforms. GO annotations related to this gene include transferase activity, transferring phosphorus-containing groups and protein tyrosine kinase activity. An important paralog of this gene is MAST3.        1. Woodfield et al. Identification of primary gene targets of TFAP2C in hormone responsive breast carcinoma cells",-6.59121218881343]
["200809_x_at","RPL12","Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L11P family of ribosomal proteins. It is located in the cytoplasm. The protein binds directly to the 26S rRNA. This gene is co-transcribed with the U65 snoRNA, which is located in its fourth intron. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. RPL12 (Ribosomal Protein L12) is a Protein Coding gene. Among its related pathways are Viral mRNA Translation and rRNA processing in the nucleus and cytosol. GO annotations related to this gene include poly(A) RNA binding and structural constituent of ribosome.         1. Burmester et. al. Pathogenicity of a viral strain (RPL12) causing avian visceral lymphomatosis and related neoplasms. II. Host-virus interrelations affecting response; 2. Crittenden et. al. Genetic influence of the Rs locus on susceptibility to avian tumor viruses. I. Neoplasms induced by RPL12 and three strains of Rous sarcoma virus\n",6.54606393117863]
["202107_s_at","MCM2","The protein encoded by this gene is one of the highly conserved mini-chromosome maintenance proteins (MCM) that are involved in the initiation of eukaryotic genome replication. The hexameric protein complex formed by MCM proteins is a key component of the pre-replication complex (pre_RC) and may be involved in the formation of replication forks and in the recruitment of other DNA replication related proteins. This protein forms a complex with MCM4, 6, and 7, and has been shown to regulate the helicase activity of the complex. This protein is phosphorylated, and thus regulated by, protein kinases CDC2 and CDC7.    1. Perou et. al. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers; 2. Sotiriou et. al. Breast cancer classification and prognosis based on gene expression profiles from a population-based study",6.52396168985597]
["65517_at","AP1M2","This gene encodes a subunit of the heterotetrameric adaptor-related protein comlex 1 (AP-1), which belongs to the adaptor complexes medium subunits family. This protein is capable of interacting with tyrosine-based sorting signals. Alternative splicing results in multiple transcript variants. Diseases associated with AP1M2 include pain agnosia and agnosia. Among its related pathways are Immune System and Infectious disease. An important paralog of this gene is AP4M1.       1. Pilarsky et. al. Activation of Wnt signalling in stroma from pancreatic cancer identified by gene expression profiling; 2. Rohan et. al. Gene Expression Profiling Separates Chromophobe Renal Cell Carcinoma from Oncocytoma and Identifies Vesicular Transport and Cell Junction Proteins as Differentially Expressed Genes",6.48729036408211]
["208767_s_at","LAPTM4B","Same as previous",-6.42792567507362]

{"sheet":"Top30_Superdelta","index":4,"n_rows":31,"n_cols":7,"rows_kept":31,"cut":false,"hidden":false,"merged":[]}
["Probe set name","Gene symbol","Annotation","Pairing probe set name","Pairing gene symbol","Annotation","Super-delta t-statistic"]
["201930_at","MCM6","MCM6 is one of the highly conserved mini-chromosome maintenance proteins (MCM) that are essential for the initiation of eukaryotic genome replication.   Link to breast cancer: 1. Van't Veer, Laura J., et al. \"Gene expression profiling predicts clinical outcome of breast cancer.\" nature 415.6871 (2002): 530-536. 2. Sotiriou, Christos, et al. \"Breast cancer classification and prognosis based on gene expression profiles from a population-based study.\" Proceedings of the National Academy of Sciences 100.18 (2003): 10393-10398.","214971_s_at","ST6GAL1","This gene encodes a member of glycosyltransferase family 29. The encoded protein is a type II membrane protein that catalyzes the transfer of sialic acid from CMP-sialic acid to galactose-containing substrates. The protein, which is normally found in the Golgi but can be proteolytically processed to a soluble form, is involved in the generation of the cell-surface carbohydrate determinants and differentiation antigens HB-6, CD75, and CD76. This gene has been incorrectly referred to as CD75. Three transcript variants encoding two different isoforms have been described. ST6GAL1 (ST6 Beta-Galactosamide Alpha-2,6-Sialyltranferase 1) is a Protein Coding gene. Diseases associated with ST6GAL1 include colon adenocarcinoma and cervical cancer, somatic. Among its related pathways are Transport to the Golgi and subsequent modification and Metabolism. GO annotations related to this gene include sialyltransferase activity and beta-galactoside alpha-2,6-sialyltransferase activity. An important paralog of this gene is ST6GAL2.      1. Cazet et. al. Tumour-associated carbohydrate antigens in \nbreast cancer; 2. Loris De Cecco et. al. Impact of biospecimens handling on biomarker research in breast cancer; 3. Hedlund et. al. α2-6–Linked Sialic Acids on N-Glycans Modulate Carcinoma Differentiation In vivo; 4. Ma et. al. Functional roles of glycogene and N-glycan in multidrug resistance of human breast cancer cells",-9.473]
["208628_s_at","YBX1","YBX1 (Y Box Binding Protein 1) is a Protein Coding gene. Diseases associated with YBX1 include liposarcoma and breast cancer. Among its related pathways are Signaling events mediated by PTP1B and Translational Control. GO annotations related to this gene include nucleic acid binding and transcription factor activity, sequence-specific DNA binding. An important paralog of this gene is YBX2.       1. Stratford, Anna L., et al. \"Y-box binding protein-1 serine 102 is a downstream target of p90 ribosomal S6 kinase in basal-like breast cancer cells.\" Breast Cancer Res 10.6 (2008): R99.","213251_at","SMARCA5","The protein encoded by this gene is a member of the SWI/SNF family of proteins. Members of this family have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The protein encoded by this gene is a component of the chromatin remodeling and spacing factor RSF, a facilitator of the transcription of class II genes by RNA polymerase II. The encoded protein is similar in sequence to the Drosophila ISWI chromatin remodeling protein. SMARCA5 (SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily A, Member 5) is a Protein Coding gene. Diseases associated with SMARCA5 include extraskeletal ewing sarcoma and williams-beuren syndrome. Among its related pathways are Cell Cycle, Mitotic and DNA Damage. GO annotations related to this gene include nucleic acid binding and hydrolase activity. An important paralog of this gene is CHD1L.      1. Liu et. al. Role of microRNAs in the Regulation of Breast Cancer Stem Cells; 2. Deng et. al. MicroRNA100 Inhibits Self-Renewal of Breast Cancer Stem–like Cells and Breast Tumor Development",-9.365]
["204962_s_at","CENPA","Centromeres are the differentiated chromosomal domains that specify the mitotic behavior of chromosomes. This gene encodes a centromere protein which contains a histone H3 related histone fold domain that is required for targeting to the centromere. Centromere protein A is proposed to be a component of a modified nucleosome or nucleosome-like structure in which it replaces 1 or both copies of conventional histone H3 in the (H3-H4)2 tetrameric core of the nucleosome particle. The protein is a replication-independent histone that is a member of the histone H3 family. Alternative splicing results in multiple transcript variants encoding distinct isoforms.         1.Sotiriou et. al. Gene Expression Profiling in Breast Cancer: Understanding the Molecular Basis of Histologic Grade To Improve Prognosis; 2. Ma et. al. Gene expression profiles of human breast cancer progression","201126_s_at","MGAT1","There are believed to be over 100 different glycosyltransferases involved in the synthesis of protein-bound and lipid-bound oligosaccharides. UDP-N-acetylglucosamine:alpha-3-D-mannoside beta-1,2-N-acetylglucosaminyltransferase I is a medial-Golgi enzyme essential for the synthesis of hybrid and complex N-glycans. The protein, encoded by a single exon, shows typical features of a type II transmembrane protein. The protein is believed to be essential for normal embryogenesis. Several variants encoding the same protein have been found for this gene. MGAT1 (Mannosyl (Alpha-1,3-)-Glycoprotein Beta-1,2-N-Acetylglucosaminyltransferase) is a Protein Coding gene. Diseases associated with MGAT1 include plague and muscle eye brain disease. Among its related pathways are Transport to the Golgi and subsequent modification and Metabolism. GO annotations related to this gene include acetylglucosaminyltransferase activity and alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity. An important paralog of this gene is POMGNT1.       1. Dennis et. al. Glycoprotein glycosylation and cancer progression; 2. Lau et. al. N-Glycans in cancer progression; 3. Karunakaran et. al. Interaction of tryptophan derivatives with SLC6A14 (ATB0,+) reveals the potential of the transporter as a drug target for cancer chemotherapy.",-8.564]
["214039_s_at","LAPTM4B","Increased expression of LAPTM4B has been found in breast, liver, lung, ovarian, uterine, gastric cancers. Elevated LAPTM4B level contributes to chemotherapy resistance in breast cancer. It was found that overexpression of LAPTM4B causes anthracyclines (doxorubicin, daunorubicin, and epirubicin) resistance by retaining drug in the cytoplasm and decreasing nuclear localization of drug and drug induced DNA damage.      1.Li et. al. Amplification of LAPTM4B and YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer","201199_s_at","PSMD1","The 26S proteasome is a multicatalytic proteinase complex with a highly ordered structure composed of 2 complexes, a 20S core and a 19S regulator. The 20S core is composed of 4 rings of 28 non-identical subunits; 2 rings are composed of 7 alpha subunits and 2 rings are composed of 7 beta subunits. The 19S regulator is composed of a base, which contains 6 ATPase subunits and 2 non-ATPase subunits, and a lid, which contains up to 10 non-ATPase subunits. Proteasomes are distributed throughout eukaryotic cells at a high concentration and cleave peptides in an ATP/ubiquitin-dependent process in a non-lysosomal pathway. An essential function of a modified proteasome, the immunoproteasome, is the processing of class I MHC peptides. This gene encodes the largest non-ATPase subunit of the 19S regulator lid, which is responsible for substrate recognition and binding. Alternatively spliced transcript variants have been found for this gene. PSMD1 (Proteasome 26S Subunit, Non-ATPase 1) is a Protein Coding gene. Among its related pathways are Immune System and Signaling by GPCR. GO annotations related to this gene include binding and enzyme regulator activity.      1. Deng et. al. Over-expression of genes and proteins of ubiquitin specific peptidases (USPs) and proteasome subunits (PSs) in breast cancer tissue observed by the methods of RFDD-PCR and proteomics",-8.56]
["208627_s_at","YBX1","same as previous","203387_s_at","TBC1D4","This gene is a member of the Tre-2/BUB2/CDC16 domain family. The protein encoded by this gene is a Rab-GTPase-activating protein, and contains two phopshotyrosine-binding domains (PTB1 and PTB2), a calmodulin-binding domain (CBD), a Rab-GTPase domain, and multiple AKT phosphomotifs. This protein is thought to play an important role in glucose homeostasis by regulating the insulin-dependent trafficking of the glucose transporter 4 (GLUT4), important for removing glucose from the bloodstream into skeletal muscle and fat tissues. Reduced expression of this gene results in an increase in GLUT4 levels at the plasma membrane, suggesting that this protein is important in intracellular retention of GLUT4 under basal conditions. When exposed to insulin, this protein is phosphorylated, dissociates from GLUT4 vesicles, resulting in increased GLUT4 at the cell surface, and enhanced glucose transport. Phosphorylation of this protein by AKT is required for proper translocation of GLUT4 to the cell surface. Individuals homozygous for a mutation in this gene are at higher risk for type 2 diabetes and have higher levels of circulating glucose and insulin levels after glucose ingestion. Alternative splicing results in multiple transcript variants encoding different isoforms. TBC1D4 (TBC1 Domain Family, Member 4) is a Protein Coding gene. Diseases associated with TBC1D4 include diabetes mellitus, noninsulin-dependent, 5 and glucose metabolism disease. Among its related pathways are Glucose / Energy Metabolism and Vesicle-mediated transport. GO annotations related to this gene include GTPase activator activity. An important paralog of this gene is RABGAP1L.        1. Naylor et. al. High resolution genomic analysis of sporadic breast cancer using array-based comparative genomic hybridization",-8.498]
["202870_s_at","CDC20","CDC20 appears to act as a regulatory protein interacting with several other proteins at multiple points in the cell cycle. It is required for two microtubule-dependent processes, nuclear movement prior to anaphase and chromosome separation.   1.Ein-Dor et. al. Outcome signature genes in breast cancer: is there a unique set? 2.Frasor et. al. Profiling of Estrogen Up- and Down-Regulated Gene Expression in Human Breast Cancer Cells: Insights into Gene Networks and Pathways Underlying Estrogenic Control of Proliferation and Cell Phenotype","208063_s_at","CAPN9","Calpains are ubiquitous, well-conserved family of calcium-dependent, cysteine proteases. The calpain proteins are heterodimers consisting of an invariant small subunit and variable large subunits. The large subunit possesses a cysteine protease domain, and both subunits possess calcium-binding domains. Calpains have been implicated in neurodegenerative processes, as their activation can be triggered by calcium influx and oxidative stress. The protein encoded by this gene is expressed predominantly in stomach and small intestine and may have specialized functions in the digestive tract. This gene is thought to be associated with gastric cancer. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. CAPN9 (Calpain 9) is a Protein Coding gene. Diseases associated with CAPN9 include gastric cancer. Among its related pathways are ERK Signaling and Apoptosis Pathway. GO annotations related to this gene include calcium ion binding and calcium-dependent cysteine-type endopeptidase activity. An important paralog of this gene is CAPNS2.       1. Rodenhiser et. al. Epigenetic mapping and functional analysis in a breast cancer metastasis model using whole-genome promoter tiling microarrays; 2. Dairkee et. al. Immutable Functional Attributes of Histologic Grade Revealed by Context-Independent Gene Expression in Primary Breast Cancer Cells",-8.433]
["213911_s_at","H2AFZ","Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Nucleosomes consist of approximately 146 bp of DNA wrapped around a histone octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. This gene encodes a replication-independent member of the histone H2A family that is distinct from other members of the family. Studies in mice have shown that this particular histone is required for embryonic development and indicate that lack of functional histone H2A leads to embryonic lethality.     1.Kreike et. al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas","201941_at","CPD","The metallocarboxypeptidase family of enzymes is divided into 2 subfamilies based on sequence similarities. The pancreatic carboxypeptidase-like and the regulatory B-type carboxypeptidase subfamilies. Carboxypeptidase D has been identified as a regulatory B-type carboxypeptidase. CPD is a homolog of duck gp180, a hepatitis B virus-binding protein. Transcript variants utilizing alternative polyadenylation signals exist for this gene. CPD (Carboxypeptidase D) is a Protein Coding gene. Diseases associated with CPD include hepatitis b. Among its related pathways are Vesicle-mediated transport and Clathrin derived vesicle budding. GO annotations related to this gene include metallocarboxypeptidase activity and serine-type carboxypeptidase activity. An important paralog of this gene is CPN1.       1. Bossi et. al. Mutant p53 gain of function: reduction of tumor malignancy of human cancer cell lines through abrogation of mutant p53 expression; 2. Leoni et. al. Indanocine, a Microtubule-Binding Indanone and a Selective Inducer of Apoptosis in Multidrug-Resistant Cancer Cells (CPD has an aliase GP180)",-8.406]
["200934_at","DEK","This gene encodes a protein with one SAP domain. This protein binds to cruciform and superhelical DNA and induces positive supercoils into closed circular DNA, and is also involved in splice site selection during mRNA processing. Chromosomal aberrations involving this region, increased expression of this gene, and the presence of antibodies against this protein are all associated with various diseases. Two transcript variants encoding different isoforms have been found for this gene.     1.Bergamaschi et. al. Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer","220547_s_at","FAM35A","FAM35A (Family With Sequence Similarity 35, Member A) is a Protein Coding gene. Not much description available.     1. Delnatte et. al. Contiguous Gene Deletion within Chromosome Arm 10q Is Associated with Juvenile Polyposis of Infancy, Reflecting Cooperation between the BMPR1A and PTEN Tumor-Suppressor Genes (This is the most relevant paper I can find)",-8.349]
["218692_at","SYBU","Syntabulin/GOLSYN is part of a kinesin motor-adaptor complex that is critical for the anterograde axonal transport of active zone components and contributes to activity-dependent presynaptic assembly during neuronal development. SYBU (Syntabulin (Syntaxin-Interacting)) is a Protein Coding gene. GO annotations related to this gene include microtubule binding and syntaxin-1 binding. An important paralog of this gene is SNPH.     1.Casa et. al. Estrogen and insulin-like growth factor-I (IGF-I) independently down-regulate critical repressors of breast cancer growth (29 cited, not many frequently cited papers)","211062_s_at","CPZ/GPR78","This gene encodes a member of the metallocarboxypeptidase family. This enzyme displays carboxypeptidase activity towards substrates with basic C-terminal residues. It is most active at neutral pH and is inhibited by active site-directed inhibitors of metallocarboxypeptidases. Alternative splicing in the coding region results in multiple transcript variants encoding different isoforms. CPZ (Carboxypeptidase Z) is a Protein Coding gene. Diseases associated with CPZ include yaws. GO annotations related to this gene include metallocarboxypeptidase activity. An important paralog of this gene is CPN1.      1. Yde et. al. The antipsychotic drug chlorpromazine enhances the cytotoxic effect of tamoxifen in tamoxifen-sensitive and tamoxifen-resistant human breast cancer cells; 2. Zhang et. al. TRAIL Resistance of Breast Cancer Cells Is Associated with Constitutive Endocytosis of Death Receptors 4 and 5",8.188]
["212736_at","C16orf45","This gene has 11 transcripts (splice variants), 1 gene allele, 62 orthologues, is a member of 1 Ensembl protein family and is associated with 5 phenotypes. C16orf45 (Chromosome 16 Open Reading Frame 45) is a Protein Coding gene. Not much literature available.   1.Partheen et. al. Expression analysis of stage III serous ovarian adenocarcinoma distinguishes a sub-group of survivors. This is the only one I can find somewhat related (ovarian is unique for women)","214695_at","UBAP2L","UBAP2L (Ubiquitin Associated Protein 2-Like) is a Protein Coding gene. GO annotations related to this gene include poly(A) RNA binding. An important paralog of this gene is UBAP2.     1. Chong et. al. Phosphoproteomics, oncogenic signaling and cancer research. Not much relevant information for this gene.",8.162]
["203554_x_at","PTTG1","PTTG1 (Pituitary Tumor-Transforming 1) is a Protein Coding gene. Diseases associated with PTTG1 include thymic hyperplasia and thyroid cancer, nonmedullary, 2. Among its related pathways are Cell Cycle, Mitotic and Integrated Pancreatic Cancer Pathway. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and cysteine-type endopeptidase inhibitor activity. An important paralog of this gene is PTTG2. Regulatory protein, which plays a central role in chromosome stability, in the p53/TP53 pathway, and DNA repair. Probably acts by blocking the action of key proteins. During the mitosis, it blocks Separase/ESPL1 function, preventing the proteolysis of the cohesin complex and the subsequent segregation of the chromosomes. At the onset of anaphase, it is ubiquitinated, conducting to its destruction and to the liberation of ESPL1. Its function is however not limited to a blocking activity, since it is required to activate ESPL1. Negatively regulates the transcriptional activity and related apoptosis activity of TP53. The negative regulation of TP53 may explain the strong transforming capability of the protein when it is overexpressed. May also play a role in DNA repair via its interaction with Ku, possibly by connecting DNA damage-response pathways with sister chromatid separation.     1. Ghayad et. al. Identification of TACC1, NOV, and PTTG1 as new candidate genes associated with endocrine therapy resistance in breast cancer","208527_x_at","HIST1H2BE","Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. The protein has antibacterial and antifungal antimicrobial activity. This gene is intronless and encodes a replication-dependent histone that is a member of the histone H2B family. Transcripts from this gene lack polyA tails but instead contain a palindromic termination element. This gene is found in the large histone gene cluster on chromosome 6. HIST1H2BE (Histone Cluster 1, H2be) is a Protein Coding gene. Among its related pathways are Signaling by GPCR and Signaling by Rho GTPases. GO annotations related to this gene include sequence-specific DNA binding and protein heterodimerization activity.      1. Ghilardi et. al. Identification of novel vascular markers through gene expression profiling of tumor-derived endothelium; 2. Joosse et. al. Genomic signature of BRCA1 deficiency in sporadic basal-like breast tumors; 3. Pardo et. al. Next-generation transcriptome sequencing of the\npremenopausal breast epithelium using specimens\nfrom a normal human breast tissue bank",-8.119]
["208767_s_at","LAPTM4B","same as previous","206582_s_at","GPR56","This gene encodes a member of the G protein-coupled receptor family and regulates brain cortical patterning. The encoded protein binds specifically to transglutaminase 2, a component of tissue and tumor stroma implicated as an inhibitor of tumor progression. Mutations in this gene are associated with a brain malformation known as bilateral frontoparietal polymicrogyria. Alternative splicing results in multiple transcript variants. ADGRG1 (Adhesion G Protein-Coupled Receptor G1, GPR56 is an aliase) is a Protein Coding gene. Diseases associated with ADGRG1 include polymicrogyria, bilateral frontoparietal and polymicrogyria, bilateral perisylvian. Among its related pathways are GPCRs, Other. GO annotations related to this gene include G-protein coupled receptor activity and collagen binding. An important paralog of this gene is ADGRG5.      1. Frasor et. al. Gene Expression Preferentially Regulated by Tamoxifen in Breast Cancer Cells and Correlations with Clinical Outcome; 2. Ai et. al. The transglutaminase 2 gene (TGM2), a potential molecular marker for chemotherapeutic drug sensitivity, is epigenetically silenced in breast cancer",-8.056]
["213664_at","SLC1A1","This gene encodes a member of the high-affinity glutamate transporters that play an essential role in transporting glutamate across plasma membranes. In brain, these transporters are crucial in terminating the postsynaptic action of the neurotransmitter glutamate, and in maintaining extracellular glutamate concentrations below neurotoxic levels. This transporter also transports aspartate, and mutations in this gene are thought to cause dicarboxylicamino aciduria, also known as glutamate-aspartate transport defect. Diseases associated with SLC1A1 include dicarboxylic aminoaciduria and schizophrenia susceptibility 18. Among its related pathways are Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds and Neuroscience. GO annotations related to this gene include L-glutamate transmembrane transporter activity and sodium:dicarboxylate symporter activity.     1. Yang et. al. Identification of a Novel Gene, GASC1, within an Amplicon at 9p23–24 Frequently Detected in Esophageal Cancer Cell Lines","201682_at","PMPCB","This gene is a member of the peptidase M16 family and encodes a protein with a zinc-binding motif. This protein is located in the mitochondrial matrix and catalyzes the cleavage of the leader peptides of precursor proteins newly imported into the mitochondria, though it only functions as part of a heterodimeric complex. PMPCB (Peptidase (Mitochondrial Processing) Beta) is a Protein Coding gene. Among its related pathways are Transport to the Golgi and subsequent modification and Mitochondrial protein import. GO annotations related to this gene include metalloendopeptidase activity. An important paralog of this gene is UQCRC1.      1. Luo et. al. Characterization of gene expression regulated by American ginseng and ginsenoside Rg3 in human colorectal cancer cells",8.055]
["204822_at","TTK","This gene encodes a dual specificity protein kinase with the ability to phosphorylate tyrosine, serine and threonine. Associated with cell proliferation, this protein is essential for chromosome alignment at the centromere during mitosis and is required for centrosome duplication. It has been found to be a critical mitotic checkpoint protein for accurate segregation of chromosomes during mitosis. Tumorigenesis may occur when this protein fails to degrade and produces excess centrosomes resulting in aberrant mitotic spindles. Alternative splicing results in multiple transcript variants.    1. Lehmann et. al. Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies","208310_s_at","C7orf28B/CCZ1","CCZ1B (CCZ1 Homolog B, Vacuolar Protein Trafficking And Biogenesis Associated) is a Protein Coding gene. An important paralog of this gene is CCZ1.     1. Nikas et. al. Linear Discriminant Functions in connection with the \nmicro-RnA Diagnosis of colon cancer",-8.022]
["203358_s_at","EZH2","This gene encodes a member of the Polycomb-group (PcG) family. PcG family members form multimeric protein complexes, which are involved in maintaining the transcriptional repressive state of genes over successive cell generations. This protein associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. This protein may play a role in the hematopoietic and central nervous systems. Multiple alternatively splcied transcript variants encoding distinct isoforms have been identified for this gene. Diseases associated with EZH2 include periodic fever, aphthous stomatitis, pharyngitis and adenitis and weaver syndrome.  1. Kleer et. al. EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells","203611_at","TERF2","This gene encodes a telomere specific protein, TERF2, which is a component of the telomere nucleoprotein complex. This protein is present at telomeres in metaphase of the cell cycle, is a second negative regulator of telomere length and plays a key role in the protective activity of telomeres. While having similar telomere binding activity and domain organization, TERF2 differs from TERF1 in that its N terminus is basic rather than acidic. TERF2 (Telomeric Repeat Binding Factor 2) is a Protein Coding gene. Diseases associated with TERF2 include werner syndrome. Among its related pathways are Apoptotic Pathways in Synovial Fibroblasts and Cell Cycle, Mitotic. GO annotations related to this gene include protein homodimerization activity and protein C-terminus binding. An important paralog of this gene is TERF1.     1. Savage et. al. Genetic variation in five genes important in telomere biology and risk for breast cancer; 2. Fridlyand et. al. Breast tumor copy number aberration phenotypes and genomic instability; 3. Shen et. al. Multiple Genetic Variants in Telomere Pathway Genes and Breast Cancer Risk;",-7.991]
["202095_s_at","BIRC5","This gene is a member of the inhibitor of apoptosis (IAP) gene family, which encode negative regulatory proteins that prevent apoptotic cell death. IAP family members usually contain multiple baculovirus IAP repeat (BIR) domains, but this gene encodes proteins with only a single BIR domain. The encoded proteins also lack a C-terminus RING finger domain. Gene expression is high during fetal development and in most tumors, yet low in adult tissues. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. Diseases associated with BIRC5 include childhood malignant schwannoma and cervical carcinosarcoma. Among its related pathways are Signaling by GPCR and Pathways in cancer.    1. Paik et. al. Gene Expression and Benefit of Chemotherapy in Women With Node-Negative, Estrogen Receptor–Positive Breast Cancer; 2. Sotiriou et. al. Gene Expression Profiling in Breast Cancer: Understanding the Molecular Basis of Histologic Grade To Improve Prognosis","203823_at","RGS3","This gene encodes a member of the regulator of G-protein signaling (RGS) family. This protein is a GTPase-activating protein that inhibits G-protein-mediated signal transduction. Alternative splicing and the use of alternative promoters results in multiple transcript variants encoding different isoforms. Long isoforms are largely cytosolic and plasma membrane-associated with a function in Wnt signaling and in the epithelial mesenchymal transition, while shorter N-terminally-truncated isoforms can be nuclear. RGS3 (Regulator Of G-Protein Signaling 3) is a Protein Coding gene. Among its related pathways are Activation of cAMP-Dependent PKA and Ephrin B reverse signaling. GO annotations related to this gene include GTPase activator activity. An important paralog of this gene is RGS18.       1. Ooe et. al. Possible involvement of CCT5, RGS3, and YKT6 genes up-regulated in p53-mutated tumors in resistance to docetaxel in human breast cancers; 2. Zhu et. al. Endothelial-specific intron-derived miR-126 is down-regulated in human breast cancer and targets both VEGFA and PIK3R2; 3. Buchholz et. al. Chemotherapy‐Induced Apoptosis and Bcl‐2 Levels Correlate with Breast Cancer Response to Chemotherapy",-7.979]
["202107_s_at","MCM2","The protein encoded by this gene is one of the highly conserved mini-chromosome maintenance proteins (MCM) that are involved in the initiation of eukaryotic genome replication. The hexameric protein complex formed by MCM proteins is a key component of the pre-replication complex (pre_RC) and may be involved in the formation of replication forks and in the recruitment of other DNA replication related proteins. This protein forms a complex with MCM4, 6, and 7, and has been shown to regulate the helicase activity of the complex. This protein is phosphorylated, and thus regulated by, protein kinases CDC2 and CDC7.    1. Perou et. al. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers; 2. Sotiriou et. al. Breast cancer classification and prognosis based on gene expression profiles from a population-based study","212270_x_at","RPL17","Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L22P family of ribosomal proteins. It is located in the cytoplasm. This gene has been referred to as rpL23 because the encoded protein shares amino acid identity with ribosomal protein L23 from Halobacterium marismortui; however, its official symbol is RPL17. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the neighboring downstream C18orf32 (chromosome 18 open reading frame 32) gene. RPL17 (Ribosomal Protein L17) is a Protein Coding gene. Among its related pathways are Infectious disease and Transport to the Golgi and subsequent modification. GO annotations related to this gene include poly(A) RNA binding and structural constituent of ribosome. An important paralog of this gene is RPL17-C18orf32.       1. Clark et. al. Identification of amplified and expressed genes in breast cancer by comparative hybridization onto microarrays of randomly selected cDNA clones; 2. Aaroe et. al. Gene expression profiling of peripheral blood\ncells for early detection of breast cancer",-7.963]
["213101_s_at","ACTR3","The specific function of this gene has not yet been determined; however, the protein it encodes is known to be a major constituent of the ARP2/3 complex. This complex is located at the cell surface and is essential to cell shape and motility through lamellipodial actin assembly and protrusion. Three transcript variants encoding two different isoforms have been found for this gene. Diseases associated with ACTR3 include wiskott-aldrich syndrome. Among its related pathways are Immune System and Signaling by GPCR.   1. Siripurapu et. al. DBC2 Significantly Influences Cell-cycle, Apoptosis, Cytoskeleton and Membrane-trafficking Pathways","212072_s_at","CSNK2A1","Casein kinase II is a serine/threonine protein kinase that phosphorylates acidic proteins such as casein. It is involved in various cellular processes, including cell cycle control, apoptosis, and circadian rhythm. The kinase exists as a tetramer and is composed of an alpha, an alpha-prime, and two beta subunits. The alpha subunits contain the catalytic activity while the beta subunits undergo autophosphorylation. The protein encoded by this gene represents the alpha subunit. While this gene is found on chromosome 20, a related transcribed pseudogene is found on chromosome 11. Three transcript variants encoding two different proteins have been found for this gene. CSNK2A1 (Casein Kinase 2, Alpha 1 Polypeptide) is a Protein Coding gene. Among its related pathways are Signaling by GPCR and Developmental Biology. GO annotations related to this gene include transferase activity, transferring phosphorus-containing groups and protein tyrosine kinase activity. An important paralog of this gene is CSNK2A2.       1. Jenssen et. al. Associations between gene expressions in breast cancer and patient survival; 2. Thewes et. al. Interference with Activator Protein-2 transcription factors leads to induction of apoptosis and an increase in chemo- and radiation-sensitivity in breast cancer cells; 3. Giroux et. al. Probing the human kinome for kinases involved in pancreatic cancer cell survival and gemcitabine resistance",-7.945]
["201088_at","KPNA2","KPNA2 protein interacts with the NLSs of DNA helicase Q1 and SV40 T antigen and may be involved in the nuclear transport of proteins. KPNA2 also may play a role in V(D)J recombination. Diseases associated with KPNA2 include ovarian endodermal sinus tumor. Among its related pathways are Immune System and Infectious disease.   1. Sotiriou et. al. Gene Expression Profiling in Breast Cancer: Understanding the Molecular Basis of Histologic Grade To Improve Prognosis; 2. Ayers et. al. Gene Expression Profiles Predict Complete Pathologic Response to Neoadjuvant Paclitaxel and Fluorouracil, Doxorubicin, and Cyclophosphamide Chemotherapy in Breast Cancer","209090_s_at","SH3GLB1","This gene encodes a SRC homology 3 domain-containing protein. The encoded protein interacts with the proapoptotic member of the Bcl-2 family, Bcl-2-associated X protein (Bax) and may be involved in regulating apoptotic signaling pathways. This protein may also be involved in maintaining mitochondrial morphology. Alternate splicing results in multiple transcript variants. SH3GLB1 (SH3-Domain GRB2-Like Endophilin B1) is a Protein Coding gene. Among its related pathways are Endocytosis and wtCFTR and delta508-CFTR traffic / Generic schema (norm and CF). GO annotations related to this gene include protein homodimerization activity and lipid binding. An important paralog of this gene is SH3GLB2.      1. Ho et. al. Novel Breast Cancer Metastasis-Associated Proteins; 2. Chen et. al. Role and regulation of autophagy in cancer; 3. Moussay et. al. The acquisition of resistance to TNFα in breast cancer cells is associated with constitutive activation of autophagy as revealed by a transcriptome analysis using a custom microarray",-7.87]
["221676_s_at","CORO1C","This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. Three transcript variants encoding two different isoforms have been found for this gene. Diseases associated with CORO1C include coronin-1a deficiency.    1. Chang et. al. Gene Expression Signature of Fibroblast Serum Response Predicts Human Cancer Progression: Similarities between Tumors and Wounds","219650_at","ERCC6L","ERCC6L (Excision Repair Cross-Complementation Group 6-Like) is a Protein Coding gene. Diseases associated with ERCC6L include bone marrow failure syndrome 2. Among its related pathways are Signaling by GPCR and Signaling by Rho GTPases. GO annotations related to this gene include nucleic acid binding and helicase activity. An important paralog of this gene is ERCC6. DNA helicase that acts as an essential component of the spindle assembly checkpoint. Contributes to the mitotic checkpoint by recruiting MAD2 to kinetochores and monitoring tension on centromeric chromatin. Acts as a tension sensor that associates with catenated DNA which is stretched under tension until it is resolved during anaphase.       1. Parshad et. al. Deficient DNA repair capacity, a predisposing factor in breast cancer; 2. Mechanic et. al. Polymorphisms in nucleotide excision repair genes, smoking and breast cancer in African Americans and whites: a population-based case–control study",-7.839]
["204170_s_at","CKS2","CKS2 protein binds to the catalytic subunit of the cyclin dependent kinases and is essential for their biological function. The CKS2 mRNA is found to be expressed in different patterns through the cell cycle in HeLa cells, which reflects specialized role for the encoded protein. Among its related pathways are Pathways in cancer and Small cell lung cancer. GO annotations related to this gene include cyclin-dependent protein serine/threonine kinase regulator activity. An important paralog of this gene is CKS1B.         1. Van't Veer, Laura J., et al. \"Gene expression profiling predicts clinical outcome of breast cancer.\" nature 415.6871 (2002): 530-536; 2. Sotiriou et. al. Breast cancer classification and prognosis based on gene expression profiles from a population-based study","219663_s_at","TMEM121","TMEM121 (Transmembrane Protein 121) is a Protein Coding gene. May play a role in MAPK signaling.    1. Sfakianakis et. al. On the Identification of Circulating Tumor Cells in Breast Cancer; Not much information for this gene, but still can find this paper somewhat relevant.",-7.696]
["203625_x_at","SKP2","This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbls class; in addition to an F-box, this protein contains 10 tandem leucine-rich repeats. This protein is an essential element of the cyclin A-CDK2 S-phase kinase. It specifically recognizes phosphorylated cyclin-dependent kinase inhibitor 1B (CDKN1B, also referred to as p27 or KIP1) predominantly in S phase and interacts with S-phase kinase-associated protein 1 (SKP1 or p19). In addition, this gene is established as a protooncogene causally involved in the pathogenesis of lymphomas. Alternative splicing of this gene generates three transcript variants encoding different isoforms. Diseases associated with SKP2 include clear cell adenofibroma and cervical squamous cell carcinoma. Among its related pathways are Immune System and Pathways in cancer. GO annotations related to this gene include identical protein binding and ubiquitin-protein transferase activity.         1. Van De Vijver et. al. A Gene-Expression Signature as a Predictor of Survival in Breast Cancer; 2. Signoretti et. al. Oncogenic role of the ubiquitin ligase subunit Skp2 in human breast cancer","202176_at","ERCC3","This gene encodes an ATP-dependent DNA helicase that functions in nucleotide excision repair. The encoded protein is a subunit of basal transcription factor 2 (TFIIH) and, therefore, also functions in class II transcription. Mutations in this gene are associated with Xeroderma pigmentosum B, Cockayne's syndrome, and trichothiodystrophy. Alternative splicing results in multiple transcript variants. ERCC3 (Excision Repair Cross-Complementation Group 3) is a Protein Coding gene. Diseases associated with ERCC3 include xeroderma pigmentosum, group b and trichothiodystrophy 2, photosensitive. Among its related pathways are Infectious disease and DNA Damage. GO annotations related to this gene include protein kinase activity and hydrolase activity.      1. Parshad et. al. Deficient DNA repair capacity, a predisposing factor in breast cancer; 2. Fan et. al. Disruption of p53 Function Sensitizes Breast Cancer MCF-7 Cells to Cisplatin and Pentoxifylline; 3. Altaha et. al. Excision repair cross complementing-group 1: Gene expression and platinum resistance (Review) parameters in human breast cancer; 4. Yen et. al. Enhanced host cell reactivation capacity and expression of DNA repair genes in human breast cancer cells resistant to bi-functional alkylating agents",-7.686]
["202705_at","CCNB2","Cyclin B2 is a member of the cyclin family, specifically the B-type cyclins. The B-type cyclins, B1 and B2, associate with p34cdc2 and are essential components of the cell cycle regulatory machinery. B1 and B2 differ in their subcellular localization. Cyclin B1 co-localizes with microtubules, whereas cyclin B2 is primarily associated with the Golgi region. Cyclin B2 also binds to transforming growth factor beta RII and thus cyclin B2/cdc2 may play a key role in transforming growth factor beta-mediated cell cycle control. Diseases associated with CCNB2 include anauxetic dysplasia and breast cancer. Among its related pathways are GPCR Pathway and Regulation of PLK1 Activity at G2/M Transition. GO annotations related to this gene include protein kinase binding. An important paralog of this gene is CCND2.        1. Bertucci et. al. Gene Expression Profiling for Molecular Characterization of Inflammatory Breast Cancer and Prediction of Response to Chemotherapy; 2. Oh et. al. Estrogen-Regulated Genes Predict Survival in Hormone Receptor–Positive Breast Cancers","213051_at","ZC3HAV1","This gene encodes a CCCH-type zinc finger protein that is thought to prevent infection by retroviruses. Studies of the rat homolog indicate that the protein may primarily function to inhibit viral gene expression and induce an innate immunity to viral infection. Alternative splicing occurs at this locus and two variants, each encoding distinct isoforms, are described. ZC3HAV1 (Zinc Finger CCCH-Type, Antiviral 1) is a Protein Coding gene. GO annotations related to this gene include poly(A) RNA binding and NAD+ ADP-ribosyltransferase activity. An important paralog of this gene is PARP14.       1. Buraschi et. al. Decorin Protein Core Affects the Global Gene Expression Profile of the Tumor Microenvironment in a Triple-Negative Orthotopic Breast Carcinoma Xenograft Model; 2. Nassa et. al. A large set of estrogen receptor β-interacting proteins identified by tandem affinity purification in hormone-responsive human breast cancer cell nuclei; 3. Einbond et. al. Carnosic acid inhibits the growth of ER-negative human breast cancer cells and synergizes with curcumin",-7.637]
["201890_at","RRM2","This gene encodes one of two non-identical subunits for ribonucleotide reductase. This reductase catalyzes the formation of deoxyribonucleotides from ribonucleotides. Synthesis of the encoded protein (M2) is regulated in a cell-cycle dependent fashion. Transcription from this gene can initiate from alternative promoters, which results in two isoforms that differ in the lengths of their N-termini. Related pseudogenes have been identified on chromosomes 1 and X. Diseases associated with RRM2 include pancreas adenocarcinoma and gestational trophoblastic neoplasm. Among its related pathways are Cell Cycle, Mitotic and Metabolism. GO annotations related to this gene include oxidoreductase activity and ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor. An important paralog of this gene is RRM2B.       1. Coser et. al. Global analysis of ligand sensitivity of estrogen inducible and suppressible genes in MCF7/BUS breast cancer cells by DNA microarray; 2. Ma et. al. A Five-Gene Molecular Grade Index and HOXB13:IL17BR Are Complementary Prognostic Factors in Early Stage Breast Cancer","207416_s_at","NFATC3","The product of this gene is a member of the nuclear factors of activated T cells DNA-binding transcription complex. This complex consists of at least two components: a preexisting cytosolic component that translocates to the nucleus upon T cell receptor (TCR) stimulation and an inducible nuclear component. Other members of this family participate to form this complex also. The product of this gene plays a role in the regulation of gene expression in T cells and immature thymocytes. Several transcript variants encoding distinct isoforms have been identified for this gene. NFATC3 (Nuclear Factor Of Activated T-Cells, Cytoplasmic, Calcineurin-Dependent 3) is a Protein Coding gene. Among its related pathways are MAPK signaling pathway and Immune System. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and RNA polymerase II core promoter proximal region sequence-specific DNA binding. An important paralog of this gene is NFATC4.      1. Jansen et. al. Molecular Classification of Tamoxifen-Resistant Breast Carcinomas by Gene Expression Profiling; 2. Siamakpour-Reihani et. al. The Role of Calcineurin/NFAT in SFRP2 Induced Angiogenesis—A Rationale for Breast Cancer Treatment with the Calcineurin Inhibitor Tacrolimus",-7.632]
["214440_at","NAT1","This gene is one of two arylamine N-acetyltransferase (NAT) genes in the human genome, and is orthologous to the mouse and rat Nat2 genes. The enzyme encoded by this gene catalyzes the transfer of an acetyl group from acetyl-CoA to various arylamine and hydrazine substrates. This enzyme helps metabolize drugs and other xenobiotics, and functions in folate catabolism. Multiple transcript variants encoding different isoforms have been found for this gene. Diseases associated with NAT1 include orthostatic intolerance and colorectal adenoma. Among its related pathways are Metabolism and Chemical carcinogenesis. GO annotations related to this gene include acetyltransferase activity and arylamine N-acetyltransferase activity. An important paralog of this gene is NAT2.         1. Dunning et. al. A Systematic Review Of Genetic Polymorphisms and Breast Cancer Risk; 2. Krajinovic et. al. Genetic susceptibility to breast cancer in French-Canadians: Role of carcinogen-metabolizing enzymes and gene–environment interactions; 3. Deitz et. al. N-Acetyltransferase-2 Genetic Polymorphism, Well-done Meat Intake, and Breast Cancer Risk among Postmenopausal Women","212694_s_at","PCCB","The protein encoded by this gene is a subunit of the propionyl-CoA carboxylase (PCC) enzyme, which is involved in the catabolism of propionyl-CoA. PCC is a mitochondrial enzyme that probably acts as a dodecamer of six alpha subunits and six beta subunits. This gene encodes the beta subunit of PCC. Defects in this gene are a cause of propionic acidemia type II (PA-2). Multiple transcript variants encoding different isoforms have been found for this gene. PCCB (Propionyl CoA Carboxylase, Beta Polypeptide) is a Protein Coding gene. Diseases associated with PCCB include pccb-related propionic acidemia and propionicacidemia. Among its related pathways are Infectious disease and Metabolism. GO annotations related to this gene include ligase activity and propionyl-CoA carboxylase activity. An important paralog of this gene is MCCC2.      1. Ali et. al. Presence of Two Members of c-erbA Receptor Gene Family (c-erbAβ and c-erbA2) in Smallest Region of Somatic Homozygosity on Chromosome 3p21–p25 in Human Breast Carcinoma; 2. Chong et. al. Phosphoproteomics, oncogenic signaling and cancer research; 3. Wen et. al. Ellagitannin (BJA3121), an anti-proliferative natural polyphenol compound, can regulate the expression of MiRNAs in HepG2 cancer cells",7.627]
["202413_s_at","USP1","This gene encodes a member of the ubiquitin-specific processing (UBP) family of proteases that is a deubiquitinating enzyme (DUB) with His and Cys domains. This protein is located in the cytoplasm and cleaves the ubiquitin moiety from ubiquitin-fused precursors and ubiquitinylated proteins. The protein specifically deubiquitinates a protein in the Fanconi anemia (FA) DNA repair pathway. Alternate transcriptional splice variants have been characterized. Diseases associated with USP1 include fanconi anemia, complementation group a. Among its related pathways are DNA Damage and DNA damage_ATM/ATR regulation of G1/S checkpoint. GO annotations related to this gene include cysteine-type endopeptidase activity and ubiquitinyl hydrolase activity. An important paralog of this gene is USP12.       1. Schwartz et. al. Susceptibility Pathways in Fanconi's Anemia and Breast Cancer; 2. Deng et. al. Over-expression of genes and proteins of ubiquitin specific peptidases (USPs) and proteasome subunits (PSs) in breast cancer tissue observed by the methods of RFDD-PCR and proteomics","202014_at","PPP1R15A","This gene is a member of a group of genes whose transcript levels are increased following stressful growth arrest conditions and treatment with DNA-damaging agents. The induction of this gene by ionizing radiation occurs in certain cell lines regardless of p53 status, and its protein response is correlated with apoptosis following ionizing radiation. [provided by RefSeq, Jul 2008]. PPP1R15A (Protein Phosphatase 1 Regulatory Subunit 15A) is a Protein Coding gene. Among its related pathways are Signaling by GPCR and GPCR Pathway. GO annotations related to this gene include protein kinase binding and protein phosphatase type 1 regulator activity.          1. Bulavin et. al. Amplification of PPM1D in human tumors abrogates p53 tumor-suppressor activity; 2. Tan et. al. Pharmacologic disruption of Polycomb-repressive complex 2-mediated gene repression selectively induces apoptosis in cancer cells; 3. Hernández-Vargas et. al. Gene expression profiling of breast cancer cells in response to gemcitabine: NF-κB pathway activation as a potential mechanism of resistance",-7.596]
["204703_at","IFT88","This gene encodes a member of the tetratrico peptide repeat (TPR) family. Mutations of a similar gene in mouse can cause polycystic kidney disease. Two transcript variants encoding distinct isoforms have been identified for this gene. Diseases associated with IFT88 include orofaciodigital syndrome i and polycystic kidney disease. Among its related pathways are Signaling by GPCR and Organelle biogenesis and maintenance. GO annotations related to this gene include kinesin binding.    1. Kuehn et. al. von Hippel-Lindau: A Tumor Suppressor Links Microtubules to Ciliogenesis and Cancer Development","219467_at","GIN1","GIN1 (Gypsy Retrotransposon Integrase 1) is a Protein Coding gene. Diseases associated with GIN1 include Parametritis. GO annotations related to this gene include nucleic acid binding.         1. Pang et. al. Analysing breast cancer microarrays from African Americans using shrinkage-based discriminant analysis",7.572]
["205509_at","CPB1","Three different procarboxypeptidases A and two different procarboxypeptidases B have been isolated. The B1 and B2 forms differ from each other mainly in isoelectric point. Carboxypeptidase B1 is a highly tissue-specific protein and is a useful serum marker for acute pancreatitis and dysfunction of pancreatic transplants. It is not elevated in pancreatic carcinoma. Diseases associated with CPB1 include acute pancreatitis and tricuspid valve insufficiency. Among its related pathways are Transport to the Golgi and subsequent modification and Pancreatic secretion. GO annotations related to this gene include metallocarboxypeptidase activity and carboxypeptidase activity. An important paralog of this gene is CPA3.         1. Carlsson et. al. Cluster analysis of S100 gene expression and genes correlating to psoriasin (S100A7) expression at different stages of breast cancer development","218628_at","CCDC53","CCDC53 (Coiled-Coil Domain Containing 53) is a Protein Coding gene. Diseases associated with CCDC53 include Wiskott-Aldrich Syndrome. Among its related pathways are Endocytosis.         1. Bert et. al. Regional Activation of the Cancer Genome by Long-Range Epigenetic Remodeling",7.549]
["218437_s_at","LZTFL1","This gene encodes a ubiquitously expressed protein that localizes to the cytoplasm. This protein interacts with Bardet-Biedl Syndrome (BBS) proteins and, through its interaction with BBS protein complexes, regulates protein trafficking to the ciliary membrane. Nonsense mutations in this gene cause a form of Bardet-Biedl Syndrome; a ciliopathy characterized in part by polydactyly, obesity, cognitive impairment, hypogonadism, and kidney failure. This gene may also function as a tumor suppressor; possibly by interacting with E-cadherin and the actin cytoskeleton and thereby regulating the transition of epithelial cells to mesenchymal cells. Alternative splicing of this gene results in multiple transcript variants. Diseases associated with LZTFL1 include bardet-biedl syndrome 17 and lztfl1- related bardet-biedl syndrome. Among its related pathways are Organelle biogenesis and maintenance and Cargo trafficking to the periciliary membrane. GO annotations related to this gene include identical protein binding and protein complex binding.     1. Chanrion et. al. A Gene Expression Signature that Can Predict the Recurrence of Tamoxifen-Treated Primary Breast Cancer","201962_s_at","RNF41","This gene encodes an E3 ubiquitin ligase. The encoded protein plays a role in type 1 cytokine receptor signaling by controlling the balance between JAK2-associated cytokine receptor degradation and ectodomain shedding. Alternative splicing results in multiple transcript variants. RNF41 (Ring Finger Protein 41) is a Protein Coding gene. Among its related pathways are Signaling by GPCR and Signaling by ERBB2. GO annotations related to this gene include ubiquitin-protein transferase activity and acid-amino acid ligase activity. An important paralog of this gene is RNF151.          1. Jing et. al. E3 ligase FLRF (Rnf41) regulates differentiation of hematopoietic progenitors by governing steady-state levels of cytokine and retinoic acid receptors; 2. Kamal et. al. Proteomic analysis of the effect of retinoic acids on the human breast cancer cell line MCF-7",7.509]
["200996_at","ACTR3","Same as previous","209477_at","EMD","Emerin is a serine-rich nuclear membrane protein and a member of the nuclear lamina-associated protein family. It mediates membrane anchorage to the cytoskeleton. Dreifuss-Emery muscular dystrophy is an X-linked inherited degenerative myopathy resulting from mutation in the emerin gene. EMD (Emerin) is a Protein Coding gene. Diseases associated with EMD include Emery-Dreifuss Muscular Dystrophy 1, X-Linked and Emery-Dreifuss Muscular Dystrophy, X-Linked. Among its related pathways are Regulation of Glucokinase by Glucokinase Regulatory Protein and Cytoskeletal Signaling. GO annotations related to this gene include actin binding and beta-tubulin binding.        1. Nahta et. al. Insulin-like Growth Factor-I Receptor/Human Epidermal Growth Factor Receptor 2 Heterodimerization Contributes to Trastuzumab Resistance of Breast Cancer Cells; 2. Hazan et. al. Exogenous Expression of N-Cadherin in Breast Cancer Cells Induces Cell Migration, Invasion, and Metastasis",-7.485]