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Volumn 5, Issue , 2015, Pages

Evaluation and integration of cancer gene classifiers: Identification and ranking of plausible drivers

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Indexed keywords

TUMOR PROTEIN;

EID: 84929153265     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep10204     Document Type: Article
Times cited : (24)

References (60)
  • 1
    • 79952284127 scopus 로고    scopus 로고
    • Hallmarks of Cancer: The Next Generation
    • Hanahan, D. & Weinberg, R. A. Hallmarks of Cancer: The Next Generation. Cell 144, 646-674 (2011).
    • (2011) Cell , vol.144 , pp. 646-674
    • Hanahan, D.1    Weinberg, R.A.2
  • 2
    • 54549108740 scopus 로고    scopus 로고
    • Comprehensive genomic characterization defnes human glioblastoma genes and core pathways
    • Chin, L. et al. Comprehensive genomic characterization defnes human glioblastoma genes and core pathways. Nature 455, 1061-1068 (2008).
    • (2008) Nature , vol.455 , pp. 1061-1068
    • Chin, L.1
  • 3
    • 77951115122 scopus 로고    scopus 로고
    • International network of cancer genome projects
    • Hudson, T. J. et al. International network of cancer genome projects. Nature 464, 993-998 (2010).
    • (2010) Nature , vol.464 , pp. 993-998
    • Hudson, T.J.1
  • 4
    • 33947101019 scopus 로고    scopus 로고
    • Patterns of somatic mutation in human cancer genomes
    • Greenman, C. et al. Patterns of somatic mutation in human cancer genomes. Nature 446, 153-158 (2007).
    • (2007) Nature , vol.446 , pp. 153-158
    • Greenman, C.1
  • 6
    • 84864598664 scopus 로고    scopus 로고
    • MuSiC: Identifying mutational signifcance in cancer genomes
    • Dees, N. D. et al. MuSiC: Identifying mutational signifcance in cancer genomes. Genome. Res. 22, 1589-1598 (2012).
    • (2012) Genome. Res. , vol.22 , pp. 1589-1598
    • Dees, N.D.1
  • 7
    • 84880507665 scopus 로고    scopus 로고
    • Mutational heterogeneity in cancer and the search for new cancer-associated genes
    • Lawrence, M. S. et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214-218 (2013).
    • (2013) Nature , vol.499 , pp. 214-218
    • Lawrence, M.S.1
  • 8
    • 78651439545 scopus 로고    scopus 로고
    • Identifying cancer driver genes in tumor genome sequencing studies
    • Youn, A. & Simon, R. Identifying cancer driver genes in tumor genome sequencing studies. Bioinformatics 27, 175-181 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 175-181
    • Youn, A.1    Simon, R.2
  • 9
  • 10
    • 84883467378 scopus 로고    scopus 로고
    • Exploiting the positional clustering of somatic mutations to identify cancer genes
    • Tamborero, D., Gonzalez-Perez, A. & Lopez-Bigas, N. OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes. Bioinformatics 29, 2238-2244 (2013).
    • (2013) Bioinformatics , vol.29 , pp. 2238-2244
    • Tamborero, D.1    Gonzalez-Perez, A.2    Oncodriveclust, L.N.3
  • 11
    • 84907372710 scopus 로고    scopus 로고
    • Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers
    • Reimand, J. & Bader, G. D. Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers. Mol. Syst. Biol. 10, 5633; DOI:10.15252/msb.20145633 (2014).
    • (2014) Mol. Syst. Biol. , vol.10 , pp. 5633
    • Reimand, J.1    Bader, G.D.2
  • 12
    • 76249105279 scopus 로고    scopus 로고
    • Genome-wide prioritization of disease genes and identifcation of disease-disease associations from an integrated human functional linkage network
    • Linghu, B., Snitkin, E. S., Hu, Z., Xia, Y. & Delisi, C. Genome-wide prioritization of disease genes and identifcation of disease-disease associations from an integrated human functional linkage network. Genome. biology 10, R91; DOI:10.1186/gb-2009-10-9-r91 (2009).
    • (2009) Genome. Biology , vol.10 , pp. R91
    • Linghu, B.1    Snitkin, E.S.2    Hu, Z.3    Xia, Y.4    Delisi, C.5
  • 13
    • 77949446630 scopus 로고    scopus 로고
    • Automated Network Analysis Identifes Core Pathways in Glioblastoma
    • Cerami, E., Demir, E., Schultz, N., Taylor, B. S. & Sander, C. Automated Network Analysis Identifes Core Pathways in Glioblastoma. Plos. One 5, e8918; doi:10.1371/journal.pone.0008918 (2010).
    • (2010) Plos. One , vol.5 , pp. e8918
    • Cerami, E.1    Demir, E.2    Schultz, N.3    Taylor, B.S.4    Sander, C.5
  • 14
    • 84856535081 scopus 로고    scopus 로고
    • Mutual exclusivity analysis identifes oncogenic network modules
    • Ciriello, G., Cerami, E., Sander, C. & Schultz, N. Mutual exclusivity analysis identifes oncogenic network modules. Genome. Res. 22, 398-406 (2012).
    • (2012) Genome. Res. , vol.22 , pp. 398-406
    • Ciriello, G.1    Cerami, E.2    Sander, C.3    Schultz, N.4
  • 15
    • 84856532705 scopus 로고    scopus 로고
    • De novo discovery of mutated driver pathways in cancer
    • Vandin, F., Upfal, E. & Raphael, B. J. De novo discovery of mutated driver pathways in cancer. Genome. Res. 22, 375-385 (2012).
    • (2012) Genome. Res. , vol.22 , pp. 375-385
    • Vandin, F.1    Upfal, E.2    Raphael, B.J.3
  • 16
    • 84904270668 scopus 로고    scopus 로고
    • Identifcation of collaborative driver pathways in breast cancer
    • Liu, Y. & Hu, Z. Identifcation of collaborative driver pathways in breast cancer. BMC genomics 15, 605 (2014).
    • (2014) BMC Genomics , vol.15 , pp. 605
    • Liu, Y.1    Hu, Z.2
  • 17
    • 84885129618 scopus 로고    scopus 로고
    • Comprehensive identifcation of mutational cancer driver genes across 12 tumor types
    • Tamborero, D. et al. Comprehensive identifcation of mutational cancer driver genes across 12 tumor types. Sci. Rep. 3, 2650; DOI:10.1038/srep02650 (2013).
    • (2013) Sci. Rep. , vol.3 , pp. 2650
    • Tamborero, D.1
  • 18
    • 84891757926 scopus 로고    scopus 로고
    • DriverDB: An exome sequencing database for cancer driver gene identifcation
    • Cheng, W. C. et al. DriverDB: an exome sequencing database for cancer driver gene identifcation. Nucleic Acids Res. 42, D1048-D1054 (2014).
    • (2014) Nucleic Acids Res. , vol.42 , pp. D1048-D1054
    • Cheng, W.C.1
  • 19
    • 33845703344 scopus 로고    scopus 로고
    • What is a support vector machine?
    • Noble, W. S. What is a support vector machine? Nat. Biotechnol. 24, 1565-1567 (2006).
    • (2006) Nat. Biotechnol. , vol.24 , pp. 1565-1567
    • Noble, W.S.1
  • 21
    • 77956864585 scopus 로고    scopus 로고
    • Shrunken methodology to genome-wide SNPs selection and construction of SNPs networks
    • Liu, Y. & Ng, M. Shrunken methodology to genome-wide SNPs selection and construction of SNPs networks. BMC systems biology 4 Suppl 2, S5; DOI:10.1186/1752-0509-4-S2-S5 (2010).
    • (2010) BMC Systems Biology , vol.4 , pp. S5
    • Liu, Y.1    Ng, M.2
  • 22
    • 84866484354 scopus 로고    scopus 로고
    • SNP Selection and Classifcation of Genome-Wide SNP Data Using Stratifed Sampling Random Forests
    • Wu, Q. Y., Ye, Y. M., Liu, Y. & Ng, M. K. SNP Selection and Classifcation of Genome-Wide SNP Data Using Stratifed Sampling Random Forests. Ieee T Nanobiosci. 11, 216-227 (2012).
    • (2012) Ieee T Nanobiosci. , vol.11 , pp. 216-227
    • Wu, Q.Y.1    Ye, Y.M.2    Liu, Y.3    Ng, M.K.4
  • 23
    • 0033569406 scopus 로고    scopus 로고
    • Molecular classifcation of cancer: Class discovery and class prediction by gene expression monitoring
    • Golub, T. R. et al. Molecular classifcation of cancer: Class discovery and class prediction by gene expression monitoring. Science 286, 531-537 (1999).
    • (1999) Science , vol.286 , pp. 531-537
    • Golub, T.R.1
  • 24
    • 33751334830 scopus 로고    scopus 로고
    • Machine learning methods for transcription data integration
    • Holloway, D. T., Kon, M. A. & DeLisi, C. Machine learning methods for transcription data integration. Ibm. J. Res. Dev. 50, 631-643 (2006).
    • (2006) Ibm. J. Res. Dev. , vol.50 , pp. 631-643
    • Holloway, D.T.1    Kon, M.A.2    Delisi, C.3
  • 25
    • 47949090070 scopus 로고    scopus 로고
    • In silico regulatory analysis for exploring human disease progression
    • Holloway, D. T., Kon, M. & DeLisi, C. In silico regulatory analysis for exploring human disease progression. Biology direct 3, 24; DOI:10.1186/1745-6150-3-24 (2008).
    • (2008) Biology Direct , vol.3 , pp. 24
    • Holloway, D.T.1    Kon, M.2    Delisi, C.3
  • 26
    • 84877028141 scopus 로고    scopus 로고
    • Comprehensive molecular portraits of human breast tumours
    • Koboldt, D. C. et al. Comprehensive molecular portraits of human breast tumours. Nature 490, 61-70 (2012).
    • (2012) Nature , vol.490 , pp. 61-70
    • Koboldt, D.C.1
  • 27
    • 79959838081 scopus 로고    scopus 로고
    • Integrated genomic analyses of ovarian carcinoma
    • Bell, D. et al. Integrated genomic analyses of ovarian carcinoma. Nature 474, 609-615 (2011).
    • (2011) Nature , vol.474 , pp. 609-615
    • Bell, D.1
  • 28
    • 84906554359 scopus 로고    scopus 로고
    • NCG 4.0: The network of cancer genes in the era of massive mutational screenings of cancer genomes
    • An, O. et al. NCG 4.0: the network of cancer genes in the era of massive mutational screenings of cancer genomes. Database 2014, bau015; DOI:10.1093/database/bau015 (2014).
    • (2014) Database , vol.2014 , pp. bau015
    • An, O.1
  • 29
    • 84891790401 scopus 로고    scopus 로고
    • The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
    • Welter, D. et al. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res. 42, D1001-1006 (2014).
    • (2014) Nucleic Acids Res. , vol.42 , pp. D1001-1006
    • Welter, D.1
  • 32
    • 58549112996 scopus 로고    scopus 로고
    • Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
    • Huang, D. W., Sherman, B. T. & Lempicki, R. A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37, 1-13 (2009).
    • (2009) Nucleic Acids Res. , vol.37 , pp. 1-13
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 33
    • 84883576667 scopus 로고    scopus 로고
    • VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies
    • Hu, Z. et al. VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies. Nucleic Acids Res. 41, W225-231 (2013).
    • (2013) Nucleic Acids Res. , vol.41 , pp. W225-231
    • Hu, Z.1
  • 34
    • 84875490185 scopus 로고    scopus 로고
    • Cancer Genome Landscapes
    • Vogelstein, B. et al. Cancer Genome Landscapes. Science 339, 1546-1558 (2013).
    • (2013) Science , vol.339 , pp. 1546-1558
    • Vogelstein, B.1
  • 35
    • 84878215865 scopus 로고    scopus 로고
    • Integrated analysis of recurrent properties of cancer genes to identify novel drivers
    • D'Antonio, M. & Ciccarelli, F. D. Integrated analysis of recurrent properties of cancer genes to identify novel drivers. Genome. biology 14, R52; DOI:10.1186/gb-2013-14-5-r52 (2013).
    • (2013) Genome. Biology , vol.14 , pp. R52
    • D'Antonio, M.1    Ciccarelli, F.D.2
  • 36
    • 84870066326 scopus 로고    scopus 로고
    • The PKCtheta pathway participates in the aberrant accumulation of Fra-1 protein in invasive ER-negative breast cancer cells
    • Belguise, K. et al. The PKCtheta pathway participates in the aberrant accumulation of Fra-1 protein in invasive ER-negative breast cancer cells. Oncogene 31, 4889-4897 (2012).
    • (2012) Oncogene , vol.31 , pp. 4889-4897
    • Belguise, K.1
  • 37
    • 84872585155 scopus 로고    scopus 로고
    • Genome and Transcriptome Sequencing in Prospective Metastatic Triple-Negative Breast Cancer Uncovers Terapeutic Vulnerabilities
    • Craig, D. W. et al. Genome and Transcriptome Sequencing in Prospective Metastatic Triple-Negative Breast Cancer Uncovers Terapeutic Vulnerabilities. Mol. Cancer Ter. 12, 104-116 (2013).
    • (2013) Mol. Cancer Ter. , vol.12 , pp. 104-116
    • Craig, D.W.1
  • 38
    • 84899670455 scopus 로고    scopus 로고
    • Expression of breast cancer metastasis suppressor-1, BRMS-1, in human breast cancer and the biological impact of BRMS-1 on the migration of breast cancer cells
    • Zhang, Y. et al. Expression of breast cancer metastasis suppressor-1, BRMS-1, in human breast cancer and the biological impact of BRMS-1 on the migration of breast cancer cells. Anticancer research 34, 1417-1426 (2014).
    • (2014) Anticancer Research , vol.34 , pp. 1417-1426
    • Zhang, Y.1
  • 39
    • 84886436589 scopus 로고    scopus 로고
    • Breast cancer metastasis suppressor-1 promoter methylation in primary breast tumors and corresponding circulating tumor cells
    • Chimonidou, M., Kallergi, G., Georgoulias, V., Welch, D. R. & Lianidou, E. S. Breast cancer metastasis suppressor-1 promoter methylation in primary breast tumors and corresponding circulating tumor cells. Molecular cancer research: MCR 11, 1248-1257 (2013).
    • (2013) Molecular Cancer Research: MCR , vol.11 , pp. 1248-1257
    • Chimonidou, M.1    Kallergi, G.2    Georgoulias, V.3    Welch, D.R.4    Lianidou, E.S.5
  • 40
    • 79954457432 scopus 로고    scopus 로고
    • Methylome analysis reveals Jak-STAT pathway deregulation in putative breast cancer stem cells
    • Hernandez-Vargas, H. et al. Methylome analysis reveals Jak-STAT pathway deregulation in putative breast cancer stem cells. Epigenetics-Us 6, 429-440 (2011).
    • (2011) Epigenetics-Us , vol.6 , pp. 429-440
    • Hernandez-Vargas, H.1
  • 41
    • 70449526719 scopus 로고    scopus 로고
    • Localized and reversible TGFbeta signalling switches breast cancer cells from cohesive to single cell motility
    • Giampieri, S. et al. Localized and reversible TGFbeta signalling switches breast cancer cells from cohesive to single cell motility. Nature cell biology 11, 1287-1296 (2009).
    • (2009) Nature Cell Biology , vol.11 , pp. 1287-1296
    • Giampieri, S.1
  • 43
    • 84888275423 scopus 로고    scopus 로고
    • Regulation of adherens junction dynamics by phosphorylation switches
    • Bertocchi, C., Vaman Rao, M. & Zaidel-Bar, R. Regulation of adherens junction dynamics by phosphorylation switches. Journal of signal transduction 2012, 125295; DOI:10.1155/2012/125295 (2012).
    • (2012) Journal of Signal Transduction , vol.2012 , pp. 125295
    • Bertocchi, C.1    Vaman Rao, M.2    Zaidel-Bar, R.3
  • 44
    • 84886414343 scopus 로고    scopus 로고
    • Targeting focal adhesion kinase in ER+/HER2+ breast cancer improves trastuzumab response
    • Lazaro, G. et al. Targeting focal adhesion kinase in ER+/HER2+ breast cancer improves trastuzumab response. Endocrine-related cancer 20, 691-704 (2013).
    • (2013) Endocrine-related Cancer , vol.20 , pp. 691-704
    • Lazaro, G.1
  • 47
    • 84869884311 scopus 로고    scopus 로고
    • Neurotrophins and their receptors in breast cancer
    • Hondermarck, H. Neurotrophins and their receptors in breast cancer. Cytokine Growth F R 23, 357-365 (2012).
    • (2012) Cytokine Growth F R , vol.23 , pp. 357-365
    • Hondermarck, H.1
  • 48
    • 84883487600 scopus 로고    scopus 로고
    • Neurotrophin-3 modulates breast cancer cells and the microenvironment to promote the growth of breast cancer brain metastasis
    • Louie, E. et al. Neurotrophin-3 modulates breast cancer cells and the microenvironment to promote the growth of breast cancer brain metastasis. Oncogene 32, 4064-4077 (2013).
    • (2013) Oncogene , vol.32 , pp. 4064-4077
    • Louie, E.1
  • 49
    • 79953792348 scopus 로고    scopus 로고
    • Fyn is Induced by Ras/PI3K/Akt Signaling and is Required for Enhanced Invasion/Migration
    • Yadav, V. & Denning, M. F. Fyn Is Induced by Ras/PI3K/Akt Signaling and Is Required for Enhanced Invasion/Migration. Mol. Carcinogen 50, 346-352 (2011).
    • (2011) Mol. Carcinogen , vol.50 , pp. 346-352
    • Yadav, V.1    Denning, M.F.2
  • 50
    • 0029003828 scopus 로고
    • Protein-Kinases in Human Breast-Cancer
    • Cance, W. G. & Liu, E. T. Protein-Kinases in Human Breast-Cancer. Breast Cancer Res. Tr. 35, 105-114 (1995).
    • (1995) Breast Cancer Res. Tr. , vol.35 , pp. 105-114
    • Cance, W.G.1    Liu, E.T.2
  • 51
    • 84872191888 scopus 로고    scopus 로고
    • PKD2 and PKD3 promote prostate cancer cell invasion by modulating NF-kappaB-and HDAC1-mediated expression and activation of uPA
    • Zou, Z. et al. PKD2 and PKD3 promote prostate cancer cell invasion by modulating NF-kappaB-and HDAC1-mediated expression and activation of uPA. Journal of cell science 125, 4800-4811 (2012).
    • (2012) Journal of Cell Science , vol.125 , pp. 4800-4811
    • Zou, Z.1
  • 52
    • 79955882233 scopus 로고    scopus 로고
    • Analysis of the Mitogen-activated protein kinase kinase 4 (MAP2K4) tumor suppressor gene in ovarian cancer
    • Davis, S. J. et al. Analysis of the Mitogen-activated protein kinase kinase 4 (MAP2K4) tumor suppressor gene in ovarian cancer. Bmc Cancer 11, 173; DOI:10.1186/1471-2407-11-173 (2011).
    • (2011) Bmc Cancer , vol.11 , pp. 173
    • Davis, S.J.1
  • 53
    • 0037058703 scopus 로고    scopus 로고
    • Expression of mitogen-activated protein kinase phosphatase-1 (MKP-1) in primary human ovarian carcinoma
    • Denkert, C. et al. Expression of mitogen-activated protein kinase phosphatase-1 (MKP-1) in primary human ovarian carcinoma. Int. J. Cancer 102, 507-513 (2002).
    • (2002) Int. J. Cancer , vol.102 , pp. 507-513
    • Denkert, C.1
  • 54
    • 76749092270 scopus 로고    scopus 로고
    • The WEKA Data Mining Sofware: An Update
    • Hall, M. et al. The WEKA Data Mining Sofware: An Update. SIGKDD Explorations 11, 10-18 (2009).
    • (2009) SIGKDD Explorations , vol.11 , pp. 10-18
    • Hall, M.1
  • 58
    • 0035478854 scopus 로고    scopus 로고
    • Random Forests
    • Breiman, L. Random Forests. Machine Learning 45, 5-32 (2001).
    • (2001) Machine Learning , vol.45 , pp. 5-32
    • Breiman, L.1
  • 59
    • 0030211964 scopus 로고    scopus 로고
    • Bagging predictors
    • Breiman, L. Bagging predictors. Machine Learning 24, 123-140 (1996).
    • (1996) Machine Learning , vol.24 , pp. 123-140
    • Breiman, L.1


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