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Volumn 8, Issue 2, 2013, Pages

Oncodrive-CIS: A Method to Reveal Likely Driver Genes Based on the Impact of Their Copy Number Changes on Expression

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ANALYTIC METHOD; ARTICLE; CARCINOGENESIS; COMPUTER PROGRAM; COPY NUMBER VARIATION; DIPLOIDY; GENE DOSAGE; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC REGULATION; GENOTYPE; INTERNET; STATISTICAL ANALYSIS; TUMOR GENE;

EID: 84873686922     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0055489     Document Type: Article
Times cited : (26)

References (24)
  • 2
    • 20044375763 scopus 로고    scopus 로고
    • Array comparative genomic hybridization and its applications in cancer
    • Pinkel D, Albertson DG, (2005) Array comparative genomic hybridization and its applications in cancer. Nat Genet 37Suppl: S11-S17.
    • (2005) Nat Genet , vol.37
    • Pinkel, D.1    Albertson, D.G.2
  • 3
    • 84859218110 scopus 로고    scopus 로고
    • Comparative analysis of algorithms for integration of copy number and expression data
    • Louhimo R, Lepikhova T, Monni O, Hautaniemi S, (2012) Comparative analysis of algorithms for integration of copy number and expression data. Nat Methods 9: 351-355.
    • (2012) Nat Methods , vol.9 , pp. 351-355
    • Louhimo, R.1    Lepikhova, T.2    Monni, O.3    Hautaniemi, S.4
  • 4
    • 3543105225 scopus 로고    scopus 로고
    • Circular binary segmentation for the analysis of array-based DNA copy number data
    • Olshen AB, Venkatraman ES, Lucito R, Wigler M, (2004) Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5: 557-572.
    • (2004) Biostatistics , vol.5 , pp. 557-572
    • Olshen, A.B.1    Venkatraman, E.S.2    Lucito, R.3    Wigler, M.4
  • 5
    • 38049100456 scopus 로고    scopus 로고
    • Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma
    • Beroukhim R, Getz G, Nghiemphu L, Barretina J, Hsueh T, et al. (2007) Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci U S A 104: 20007-20012.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 20007-20012
    • Beroukhim, R.1    Getz, G.2    Nghiemphu, L.3    Barretina, J.4    Hsueh, T.5
  • 6
    • 84856796700 scopus 로고    scopus 로고
    • DEAD box 1 (DDX1) expression predicts for local control and overall survival in early stage, node-negative breast cancer
    • Taunk NK, Goyal S, Wu H, Moran MS, Chen S, et al. (2012) DEAD box 1 (DDX1) expression predicts for local control and overall survival in early stage, node-negative breast cancer. Cancer 118: 888-898.
    • (2012) Cancer , vol.118 , pp. 888-898
    • Taunk, N.K.1    Goyal, S.2    Wu, H.3    Moran, M.S.4    Chen, S.5
  • 7
    • 67650080623 scopus 로고    scopus 로고
    • Essential role for eIF4GI overexpression in the pathogenesis of inflammatory breast cancer
    • Silvera D, Arju R, Darvishian F, Levine PH, Zolfaghari L, et al. (2009) Essential role for eIF4GI overexpression in the pathogenesis of inflammatory breast cancer. Nat Cell Biol 11: 903-908.
    • (2009) Nat Cell Biol , vol.11 , pp. 903-908
    • Silvera, D.1    Arju, R.2    Darvishian, F.3    Levine, P.H.4    Zolfaghari, L.5
  • 8
    • 0032940198 scopus 로고    scopus 로고
    • Functional domains of c-myc promoter binding protein 1 involved in transcriptional repression and cell growth regulation
    • Ghosh AK, Steele R, Ray RB, (1999) Functional domains of c-myc promoter binding protein 1 involved in transcriptional repression and cell growth regulation. Mol Cell Biol 19: 2880-2886.
    • (1999) Mol Cell Biol , vol.19 , pp. 2880-2886
    • Ghosh, A.K.1    Steele, R.2    Ray, R.B.3
  • 9
    • 0030851904 scopus 로고    scopus 로고
    • A human homolog of the yeast Ssk2/Ssk22 MAP kinase kinase kinases, MTK1, mediates stress-induced activation of the p38 and JNK pathways
    • Takekawa M, Posas F, Saito H, (1997) A human homolog of the yeast Ssk2/Ssk22 MAP kinase kinase kinases, MTK1, mediates stress-induced activation of the p38 and JNK pathways. EMBO J 16: 4973-4982.
    • (1997) EMBO J , vol.16 , pp. 4973-4982
    • Takekawa, M.1    Posas, F.2    Saito, H.3
  • 10
    • 36749066161 scopus 로고    scopus 로고
    • ANCCA, an estrogen-regulated AAA+ ATPase coactivator for ERalpha, is required for coregulator occupancy and chromatin modification
    • Zou JX, Revenko AS, Li LB, Gemo AT, Chen HW, (2007) ANCCA, an estrogen-regulated AAA+ ATPase coactivator for ERalpha, is required for coregulator occupancy and chromatin modification. Proc Natl Acad Sci U S A 104: 18067-18072.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 18067-18072
    • Zou, J.X.1    Revenko, A.S.2    Li, L.B.3    Gemo, A.T.4    Chen, H.W.5
  • 12
    • 79961145353 scopus 로고    scopus 로고
    • Regulation of the MDM2-P53 pathway and tumor growth by PICT1 via nucleolar RPL11
    • Sasaki M, Kawahara K, Nishio M, Mimori K, Kogo R, et al. (2011) Regulation of the MDM2-P53 pathway and tumor growth by PICT1 via nucleolar RPL11. Nat Med 17: 944-951.
    • (2011) Nat Med , vol.17 , pp. 944-951
    • Sasaki, M.1    Kawahara, K.2    Nishio, M.3    Mimori, K.4    Kogo, R.5
  • 13
    • 80052575003 scopus 로고    scopus 로고
    • Integrative analysis of array-comparative genomic hybridisation and matched gene expression profiling data reveals novel genes with prognostic significance in oesophageal adenocarcinoma
    • Goh XY, Rees JR, Paterson AL, Chin SF, Marioni JC, et al. (2011) Integrative analysis of array-comparative genomic hybridisation and matched gene expression profiling data reveals novel genes with prognostic significance in oesophageal adenocarcinoma. Gut 60: 1317-1326.
    • (2011) Gut , vol.60 , pp. 1317-1326
    • Goh, X.Y.1    Rees, J.R.2    Paterson, A.L.3    Chin, S.F.4    Marioni, J.C.5
  • 14
    • 0034655991 scopus 로고    scopus 로고
    • BASC, a super complex of BRCA1-associated proteins involved in the recognition and repair of aberrant DNA structures
    • Wang Y, Cortez D, Yazdi P, Neff N, Elledge SJ, et al. (2000) BASC, a super complex of BRCA1-associated proteins involved in the recognition and repair of aberrant DNA structures. Genes Dev 14: 927-939.
    • (2000) Genes Dev , vol.14 , pp. 927-939
    • Wang, Y.1    Cortez, D.2    Yazdi, P.3    Neff, N.4    Elledge, S.J.5
  • 15
    • 79952606011 scopus 로고    scopus 로고
    • CNAmet: an R package for integrating copy number, methylation and expression data
    • Louhimo R, Hautaniemi S, (2011) CNAmet: an R package for integrating copy number, methylation and expression data. Bioinformatics 27: 887-888.
    • (2011) Bioinformatics , vol.27 , pp. 887-888
    • Louhimo, R.1    Hautaniemi, S.2
  • 16
    • 28444493739 scopus 로고    scopus 로고
    • Combining probability from independent tests: the weighted Z-method is superior to Fisher's approach
    • Whitlock MC, (2005) Combining probability from independent tests: the weighted Z-method is superior to Fisher's approach. J Evol Biol 18: 1368-1373.
    • (2005) J Evol Biol , vol.18 , pp. 1368-1373
    • Whitlock, M.C.1
  • 17
    • 26444453688 scopus 로고    scopus 로고
    • Bladder cancer stage and outcome by array-based comparative genomic hybridization
    • Blaveri E, Brewer JL, Roydasgupta R, Fridlyand J, DeVries S, et al. (2005) Bladder cancer stage and outcome by array-based comparative genomic hybridization. Clin Cancer Res 11: 7012-7022.
    • (2005) Clin Cancer Res , vol.11 , pp. 7012-7022
    • Blaveri, E.1    Brewer, J.L.2    Roydasgupta, R.3    Fridlyand, J.4    DeVries, S.5
  • 18
    • 0033931867 scopus 로고    scopus 로고
    • Assessing the accuracy of prediction algorithms for classification: an overview
    • Baldi P, Brunak S, Chauvin Y, Andersen CA, Nielsen H, (2000) Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 16: 412-424.
    • (2000) Bioinformatics , vol.16 , pp. 412-424
    • Baldi, P.1    Brunak, S.2    Chauvin, Y.3    Andersen, C.A.4    Nielsen, H.5
  • 20
    • 84856535081 scopus 로고    scopus 로고
    • Mutual exclusivity analysis identifies oncogenic network modules
    • Ciriello G, Cerami E, Sander C, Schultz N, (2012) Mutual exclusivity analysis identifies oncogenic network modules. Genome Res 22: 398-406.
    • (2012) Genome Res , vol.22 , pp. 398-406
    • Ciriello, G.1    Cerami, E.2    Sander, C.3    Schultz, N.4
  • 21
    • 54549108740 scopus 로고    scopus 로고
    • Comprehensive genomic characterization defines human glioblastoma genes and core pathways
    • The Cancer Genome Atlas Research Network
    • The Cancer Genome Atlas Research Network, (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455: 1061-1068.
    • (2008) Nature , vol.455 , pp. 1061-1068
  • 22
    • 79959838081 scopus 로고    scopus 로고
    • Integrated genomic analyses of ovarian carcinoma
    • Integrated genomic analyses of ovarian carcinoma. Nature 474: 609-615.
    • Nature , vol.474 , pp. 609-615
  • 24
    • 79955934629 scopus 로고    scopus 로고
    • Gitools: analysis and visualisation of genomic data using interactive heat-maps
    • Perez-Llamas C, Lopez-Bigas N, (2011) Gitools: analysis and visualisation of genomic data using interactive heat-maps. PLoS One 6: e19541.
    • (2011) PLoS One , vol.6
    • Perez-Llamas, C.1    Lopez-Bigas, N.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.