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Volumn 17, Issue 1, 2016, Pages

OncodriveFML: A general framework to identify coding and non-coding regions with cancer driver mutations

Author keywords

Cancer drivers; Local functional mutations bias; Non coding drivers; Non coding regions

Indexed keywords

LONG UNTRANSLATED RNA; MESSENGER RNA;

EID: 84979960214     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-016-0994-0     Document Type: Article
Times cited : (230)

References (43)
  • 2
    • 77951115122 scopus 로고    scopus 로고
    • International network of cancer genome projects
    • ICGC. International network of cancer genome projects. Nature. 2010;464:993-8.
    • (2010) Nature , vol.464 , pp. 993-998
  • 6
    • 84883467378 scopus 로고    scopus 로고
    • OncodriveCLUST: 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. 2013;29:2238-44.
    • (2013) Bioinformatics. , vol.29 , pp. 2238-2244
    • Tamborero, D.1    Gonzalez-Perez, A.2    Lopez-Bigas, N.3
  • 7
    • 84873802661 scopus 로고    scopus 로고
    • Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers
    • Reimand J, Bader GD. Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers. Mol Syst Biol. 2013;9:637.
    • (2013) Mol Syst Biol. , vol.9 , pp. 637
    • Reimand, J.1    Bader, G.D.2
  • 9
    • 84867744264 scopus 로고    scopus 로고
    • Evolution of the cancer genome
    • Yates LR, Campbell PJ. Evolution of the cancer genome. Nat Rev Genet. 2012;13:795-806.
    • (2012) Nat Rev Genet. , vol.13 , pp. 795-806
    • Yates, L.R.1    Campbell, P.J.2
  • 10
    • 84923358817 scopus 로고    scopus 로고
    • Cell-of-origin chromatin organization shapes the mutational landscape of cancer
    • Polak P, Karlic R, Koren A, Thurman R, Sandstrom R, Michael S, et al. Cell-of-origin chromatin organization shapes the mutational landscape of cancer. Nature. 2015;518:360-4.
    • (2015) Nature. , vol.518 , pp. 360-364
    • Polak, P.1    Karlic, R.2    Koren, A.3    Thurman, R.4    Sandstrom, R.5    Michael, S.6
  • 11
    • 84908894973 scopus 로고    scopus 로고
    • Genome-wide analysis of noncoding regulatory mutations in cancer
    • Weinhold N, Jacobsen A, Schultz N, Sander C, Lee W. Genome-wide analysis of noncoding regulatory mutations in cancer. Nat Genet. 2014;46:1160-5.
    • (2014) Nat Genet. , vol.46 , pp. 1160-1165
    • Weinhold, N.1    Jacobsen, A.2    Schultz, N.3    Sander, C.4    Lee, W.5
  • 12
    • 84922527340 scopus 로고    scopus 로고
    • Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types
    • Fredriksson NJ, Ny L, Nilsson JA, Larsson E. Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types. Nat Genet. 2014;46:1-7.
    • (2014) Nat Genet. , vol.46 , pp. 1-7
    • Fredriksson, N.J.1    Ny, L.2    Nilsson, J.A.3    Larsson, E.4
  • 14
    • 84949034526 scopus 로고    scopus 로고
    • LARVA: An integrative framework for large-scale analysis of recurrent variants in noncoding annotations
    • Lochovsky L, Zhang J, Fu Y, Khurana E, Gerstein M. LARVA: An integrative framework for large-scale analysis of recurrent variants in noncoding annotations. Nucleic Acids Res. 2015;43:8123-34.
    • (2015) Nucleic Acids Res. , vol.43 , pp. 8123-8134
    • Lochovsky, L.1    Zhang, J.2    Fu, Y.3    Khurana, E.4    Gerstein, M.5
  • 15
    • 84928105158 scopus 로고    scopus 로고
    • MSK-IMPACT: a hybridization capture-based next-generation sequencing clinical assay for solid tumor molecular oncology
    • Cheng DT, Mitchell T, Zehir A, Shah RH, Benayed R, Syed A, et al. MSK-IMPACT: a hybridization capture-based next-generation sequencing clinical assay for solid tumor molecular oncology. J Mol Diagn. 2015;17:251-64.
    • (2015) J Mol Diagn. , vol.17 , pp. 251-264
    • Cheng, D.T.1    Mitchell, T.2    Zehir, A.3    Shah, R.H.4    Benayed, R.5    Syed, A.6
  • 16
    • 84895858942 scopus 로고    scopus 로고
    • A general framework for estimating the relative pathogenicity of human genetic variants
    • Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J, et al. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014;46:310-5.
    • (2014) Nat Genet. , vol.46 , pp. 310-315
    • Kircher, M.1    Witten, D.M.2    Jain, P.3    O'Roak, B.J.4    Cooper, G.M.5    Shendure, J.6
  • 18
    • 84911379962 scopus 로고    scopus 로고
    • E-Driver: A novel method to identify protein regions driving cancer
    • Porta-Pardo E, Godzik A. E-Driver: A novel method to identify protein regions driving cancer. Bioinformatics. 2014;30:3109-14.
    • (2014) Bioinformatics. , vol.30 , pp. 3109-3114
    • Porta-Pardo, E.1    Godzik, A.2
  • 23
    • 84940163320 scopus 로고    scopus 로고
    • Involvement of p29/SYF2/fSAP29/NTC31 in the progression of NSCLC via modulating cell proliferation
    • Liu Y, Ni T, Xue Q, Lv L, Chen B, Cui X, et al. Involvement of p29/SYF2/fSAP29/NTC31 in the progression of NSCLC via modulating cell proliferation. Pathol Res Pract. 2015;211:36-42.
    • (2015) Pathol Res Pract. , vol.211 , pp. 36-42
    • Liu, Y.1    Ni, T.2    Xue, Q.3    Lv, L.4    Chen, B.5    Cui, X.6
  • 24
    • 84878726903 scopus 로고    scopus 로고
    • Expression of p114RhoGEF predicts lymph node metastasis and poor survival of squamous-cell lung carcinoma patients
    • Song C, Gao Y, Tian Y, Han X, Chen Y, Tian DL. Expression of p114RhoGEF predicts lymph node metastasis and poor survival of squamous-cell lung carcinoma patients. Tumor Biol. 2013;34:1925-33.
    • (2013) Tumor Biol. , vol.34 , pp. 1925-1933
    • Song, C.1    Gao, Y.2    Tian, Y.3    Han, X.4    Chen, Y.5    Tian, D.L.6
  • 25
    • 34547628200 scopus 로고    scopus 로고
    • Proteasome function is required for DNA damage response and fanconi anemia pathway activation
    • Jacquemont C, Taniguchi T. Proteasome function is required for DNA damage response and fanconi anemia pathway activation. Cancer Res. 2007;67:7395-405.
    • (2007) Cancer Res. , vol.67 , pp. 7395-7405
    • Jacquemont, C.1    Taniguchi, T.2
  • 28
    • 84956615603 scopus 로고    scopus 로고
    • Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations
    • Araya CL, Cenik C, Reuter JA, Kiss G, Pande VS, Snyder MP, et al. Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations. Nat Genet. 2016;48:117-25.
    • (2016) Nat Genet. , vol.48 , pp. 117-125
    • Araya, C.L.1    Cenik, C.2    Reuter, J.A.3    Kiss, G.4    Pande, V.S.5    Snyder, M.P.6
  • 32
    • 0029011919 scopus 로고
    • The p150 and p60 subunits of chromatin assembly factor I: a molecular link between newly synthesized histones and DNA replication
    • Kaufman PD, Kobayashi R, Kessler N, Stillman B. The p150 and p60 subunits of chromatin assembly factor I: a molecular link between newly synthesized histones and DNA replication. Cell. 1995;81:1105-14.
    • (1995) Cell. , vol.81 , pp. 1105-1114
    • Kaufman, P.D.1    Kobayashi, R.2    Kessler, N.3    Stillman, B.4
  • 35
    • 79961202865 scopus 로고    scopus 로고
    • Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression
    • Prensner JR, Iyer MK, Balbin OA, Dhanasekaran SM, Cao Q, Brenner JC, et al. Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotech. 2011;29:742-9.
    • (2011) Nat Biotech. , vol.29 , pp. 742-749
    • Prensner, J.R.1    Iyer, M.K.2    Balbin, O.A.3    Dhanasekaran, S.M.4    Cao, Q.5    Brenner, J.C.6
  • 36
    • 67650921949 scopus 로고    scopus 로고
    • Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
    • Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A. 2009;106:11667-72.
    • (2009) Proc Natl Acad Sci U S A. , vol.106 , pp. 11667-11672
    • Khalil, A.M.1    Guttman, M.2    Huarte, M.3    Garber, M.4    Raj, A.5    Rivea Morales, D.6
  • 37
    • 84879837310 scopus 로고    scopus 로고
    • MALAT1 - A paradigm for long noncoding RNA function in cancer.
    • Gutschner T, Hämmerle M, Diederichs S. MALAT1 - A paradigm for long noncoding RNA function in cancer. J Mol Med. 2013;791-801.
    • (2013) J Mol Med. , pp. 791-801
    • Gutschner, T.1    Hämmerle, M.2    Diederichs, S.3
  • 38
    • 84929991442 scopus 로고    scopus 로고
    • High burden and pervasive positive selection of somatic mutations in normal human skin
    • Martincorena I, Roshan A, Gerstung M, Ellis P, Van Loo P, McLaren S, et al. High burden and pervasive positive selection of somatic mutations in normal human skin. Science (80-). 2015;348:880-6.
    • (2015) Science (80-) , vol.348 , pp. 880-886
    • Martincorena, I.1    Roshan, A.2    Gerstung, M.3    Ellis, P.4    Loo, P.5    McLaren, S.6
  • 40
    • 84878220465 scopus 로고    scopus 로고
    • Targeted next-generation sequencing of head and neck squamous cell carcinoma identifies novel genetic alterations in HPV+ and HPV- tumors
    • Lechner M, Frampton GM, Fenton T, Feber A, Palmer G, Jay A, et al. Targeted next-generation sequencing of head and neck squamous cell carcinoma identifies novel genetic alterations in HPV+ and HPV- tumors. Genome Med. 2013;5:49.
    • (2013) Genome Med. , vol.5 , pp. 49
    • Lechner, M.1    Frampton, G.M.2    Fenton, T.3    Feber, A.4    Palmer, G.5    Jay, A.6
  • 41
    • 84901680089 scopus 로고    scopus 로고
    • Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer
    • Wang K, Yuen ST, Xu J, Lee SP, Yan HHN, Shi ST, et al. Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer. Nat Genet. 2014;46:573-82.
    • (2014) Nat Genet. , vol.46 , pp. 573-582
    • Wang, K.1    Yuen, S.T.2    Xu, J.3    Lee, S.P.4    Yan, H.H.N.5    Shi, S.T.6
  • 42
    • 84928987900 scopus 로고    scopus 로고
    • HTSeq - A Python framework to work with high-throughput sequencing data.
    • Anders S, Pyl PT, Huber W. HTSeq - A Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31:166-9.
    • (2015) Bioinformatics. , vol.31 , pp. 166-169
    • Anders, S.1    Pyl, P.T.2    Huber, W.3
  • 43
    • 84893092097 scopus 로고    scopus 로고
    • Comprehensive analysis of long non-coding RNAS in ovarian cancer reveals global patterns and targeted DNA amplification.
    • Akrami R, Jacobsen A, Hoell J, Schultz N, Sander C, Larsson E. Comprehensive analysis of long non-coding RNAS in ovarian cancer reveals global patterns and targeted DNA amplification. PLoS One. 2013;8:e80306.
    • (2013) PLoS One. , vol.8 , pp. e80306
    • Akrami, R.1    Jacobsen, A.2    Hoell, J.3    Schultz, N.4    Sander, C.5    Larsson, E.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.