Wood LD, Parsons DW, Jones S, Lin J, Sjoblom T, Leary RJ, Shen D, Boca SM, Barber T, Ptak J, et al. The genomic landscapes of human breast and colorectal cancers. Science. 2007;318:1108–13.
Article
CAS
PubMed
Google Scholar
Greenman C, Stephens P, Smith R, Dalgliesh GL, Hunter C, Bignell G, Davies H, Teague J, Butler A, Stevens C, et al. Patterns of somatic mutation in human cancer genomes. Nature. 2007;446:153–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz Jr LA, Kinzler KW. Cancer genome landscapes. Science. 2013;339:1546–58.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stratton MR, Campbell PJ, Futreal PA. The cancer genome. Nature. 2009;458:719–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008, 455:1061–1068.
Watson IR, Takahashi K, Futreal PA, Chin L. Emerging patterns of somatic mutations in cancer. Nat Rev Genet. 2013;14:703–18.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, Greenman CD, Varela I, Lin ML, Ordonez GR, Bignell GR, et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature. 2010;463:191–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Forbes SA, Beare D, Gunasekaran P, Leung K, Bindal N, Boutselakis H, Ding M, Bamford S, Cole C, Ward S, et al. COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res. 2015;43:D805–811.
Article
PubMed
PubMed Central
Google Scholar
Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, et al. Computational approaches to identify functional genetic variants in cancer genomes. Nat Methods. 2013;10:723–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA, et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature. 2013;499:214–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bignell GR, Greenman CD, Davies H, Butler AP, Edkins S, Andrews JM, Buck G, Chen L, Beare D, Latimer C, et al. Signatures of mutation and selection in the cancer genome. Nature. 2010;463:893–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gibson TJ. Cell regulation: determined to signal discrete cooperation. Trends Biochem Sci. 2009;34:471–82.
Article
CAS
PubMed
Google Scholar
van der Lee R, Buljan M, Lang B, Weatheritt RJ, Daughdrill GW, Dunker AK, Fuxreiter M, Gough J, Gsponer J, Jones DT, et al. Classification of intrinsically disordered regions and proteins. Chem Rev. 2014;114:6589–631.
Article
PubMed
PubMed Central
Google Scholar
Joerger AC, Fersht AR. Structure-function-rescue: the diverse nature of common p53 cancer mutants. Oncogene. 2007;26:2226–42.
Article
CAS
PubMed
Google Scholar
Yang F, Petsalaki E, Rolland T, Hill DE, Vidal M, Roth FP. Protein domain-level landscape of cancer-type-specific somatic mutations. PLoS Comput Biol. 2015;11:e1004147.
Article
PubMed
PubMed Central
Google Scholar
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.
Article
CAS
PubMed
Google Scholar
Porta-Pardo E, Godzik A. e-Driver: a novel method to identify protein regions driving cancer. Bioinformatics. 2014;30(3):109–3114.
Google Scholar
Porta-Pardo E, Hrabe T, Godzik A. Cancer3D: understanding cancer mutations through protein structures. Nucleic Acids Res. 2015;43:D968–973.
Article
PubMed
PubMed Central
Google Scholar
Kamburov A, Lawrence MS, Polak P, Leshchiner I, Lage K, Golub TR, Lander ES, Getz G. Comprehensive assessment of cancer missense mutation clustering in protein structures. Proc Natl Acad Sci U S A. 2015;112:E5486–5495.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nehrt NL, Peterson TA, Park D, Kann MG. Domain landscapes of somatic mutations in cancer. BMC Genomics. 2012;13(4):S9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kanai Y, Ushijima S, Nakanishi Y, Sakamoto M, Hirohashi S. Mutation of the DNA methyltransferase (DNMT) 1 gene in human colorectal cancers. Cancer Lett. 2003;192:75–82.
Article
CAS
PubMed
Google Scholar
Bozic I, Antal T, Ohtsuki H, Carter H, Kim D, Chen S, Karchin R, Kinzler KW, Vogelstein B, Nowak MA. Accumulation of driver and passenger mutations during tumor progression. Proc Natl Acad Sci U S A. 2010;107:18545–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kim MS, Chung NG, Yoo NJ, Lee SH. Somatic mutation of IL7R exon 6 in acute leukemias and solid cancers. Hum Pathol. 2013;44:551–5.
Article
CAS
PubMed
Google Scholar
Li S, Thangapazham RL, Wang JA, Rajesh S, Kao TC, Sperling L, Moss J, Darling TN. Human TSC2-null fibroblast-like cells induce hair follicle neogenesis and hamartoma morphogenesis. Nat Commun. 2011;2:235.
Article
PubMed
PubMed Central
Google Scholar
Bell DW, Sikdar N, Lee KY, Price JC, Chatterjee R, Park HD, Fox J, Ishiai M, Rudd ML, Pollock LM, et al. Predisposition to cancer caused by genetic and functional defects of mammalian Atad5. PLoS Genet. 2011;7:e1002245.
Article
CAS
PubMed
PubMed Central
Google Scholar
UniProt: a hub for protein information. Nucleic Acids Res. 2015;43:D204-212.
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, et al. Pfam: the protein families database. Nucleic Acids Res. 2014;42:D222–230.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dinkel H, Van Roey K, Michael S, Davey NE, Weatheritt RJ, Born D, Speck T, Kruger D, Grebnev G, Kuban M, et al. The eukaryotic linear motif resource ELM: 10 years and counting. Nucleic Acids Res. 2014;42:D259–266.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pajkos M, Meszaros B, Simon I, Dosztanyi Z. Is there a biological cost of protein disorder? Analysis of cancer-associated mutations. Mol BioSyst. 2012;8:296–307.
Article
CAS
PubMed
Google Scholar
Dixit A, Verkhivker GM. Structure-functional prediction and analysis of cancer mutation effects in protein kinases. Comput Math Methods Med. 2014;2014:653487.
Article
PubMed
PubMed Central
Google Scholar
Dixit A, Yi L, Gowthaman R, Torkamani A, Schork NJ, Verkhivker GM. Sequence and structure signatures of cancer mutation hotspots in protein kinases. PLoS One. 2009;4:e7485.
Article
PubMed
PubMed Central
Google Scholar
Uyar B, Weatheritt RJ, Dinkel H, Davey NE, Gibson TJ. Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer? Mol BioSyst. 2014;10:2626–42.
Article
CAS
PubMed
PubMed Central
Google Scholar
Reimand J, Wagih O, Bader GD. The mutational landscape of phosphorylation signaling in cancer. Scientific reports. 2013;3:2651.
Article
PubMed
PubMed Central
Google Scholar
Lawrence MS, Stojanov P, Mermel CH, Robinson JT, Garraway LA, Golub TR, Meyerson M, Gabriel SB, Lander ES, Getz G. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature. 2014;505:495–501.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ding L, Wendl MC, McMichael JF, Raphael BJ. Expanding the computational toolbox for mining cancer genomes. Nat Rev Genet. 2014;15:556–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tamborero D, Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Kandoth C, Reimand J, Lawrence MS, Getz G, Bader GD, Ding L, Lopez-Bigas N. Comprehensive identification of mutational cancer driver genes across 12 tumor types. Scientific reports. 2013;3:2650.
PubMed
PubMed Central
Google Scholar
Wendl MC, Wallis JW, Lin L, Kandoth C, Mardis ER, Wilson RK, Ding L. PathScan: a tool for discerning mutational significance in groups of putative cancer genes. Bioinformatics. 2011;27:1595–602.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gonzalez-Perez A, Lopez-Bigas N. Functional impact bias reveals cancer drivers. Nucleic Acids Res. 2012;40:e169.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Tamborero D, Schroeder MP, Jene-Sanz A, Santos A, Lopez-Bigas N. IntOGen-mutations identifies cancer drivers across tumor types. Nat Methods. 2013;10:1081–2.
Article
CAS
PubMed
Google Scholar
Dutta RK, Welander J, Brauckhoff M, Walz M, Alesina P, Arnesen T, Soderkvist P, Gimm O. Complementary somatic mutations of KCNJ5, ATP1A1, and ATP2B3 in sporadic aldosterone producing adrenal adenomas. Endocrine-related cancer. 2014;21:L1–4.
Article
CAS
PubMed
Google Scholar
Kraan W, Horlings HM, van Keimpema M, Schilder-Tol EJ, Oud ME, Scheepstra C, Kluin PM, Kersten MJ, Spaargaren M, Pals ST. High prevalence of oncogenic MYD88 and CD79B mutations in diffuse large B-cell lymphomas presenting at immune-privileged sites. Blood Cancer J. 2013;3:e139.
Article
CAS
PubMed
PubMed Central
Google Scholar
Robinson DR, Wu YM, Vats P, Su F, Lonigro RJ, Cao X, Kalyana-Sundaram S, Wang R, Ning Y, Hodges L, et al. Activating ESR1 mutations in hormone-resistant metastatic breast cancer. Nat Genet. 2013;45:1446–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kakiuchi M, Nishizawa T, Ueda H, Gotoh K, Tanaka A, Hayashi A, Yamamoto S, Tatsuno K, Katoh H, Watanabe Y, et al. Recurrent gain-of-function mutations of RHOA in diffuse-type gastric carcinoma. Nat Genet. 2014;46:583–7.
Article
CAS
PubMed
Google Scholar
Maxson JE, Gotlib J, Pollyea DA, Fleischman AG, Agarwal A, Eide CA, Bottomly D, Wilmot B, McWeeney SK, Tognon CE, et al. Oncogenic CSF3R mutations in chronic neutrophilic leukemia and atypical CML. N Engl J Med. 2013;368:1781–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nagarajan N, Bertrand D, Hillmer AM, Zang ZJ, Yao F, Jacques PE, Teo AS, Cutcutache I, Zhang Z, Lee WH, et al. Whole-genome reconstruction and mutational signatures in gastric cancer. Genome Biol. 2012;13:R115.
Article
PubMed
PubMed Central
Google Scholar
Leir SH, Harris A. MUC6 mucin expression inhibits tumor cell invasion. Exp Cell Res. 2011;317:2408–19.
Article
CAS
PubMed
Google Scholar
de Bolos C, Guma M, Barranco C, Garrido M, Kim YS, Real FX. MUC6 expression in breast tissues and cultured cells: abnormal expression in tumors and regulation by steroid hormones. Intern J Cancer J Intern du Cancer. 1998;77:193–9.
Article
Google Scholar
Kim N, Hong Y, Kwon D, Yoon S. Somatic mutaome profile in human cancer tissues. Genome Inform. 2013;11:239–44.
Article
Google Scholar
Lee KY, Fu H, Aladjem MI, Myung K. ATAD5 regulates the lifespan of DNA replication factories by modulating PCNA level on the chromatin. J Cell Biol. 2013;200:31–44.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pilati C, Letouze E, Nault JC, Imbeaud S, Boulai A, Calderaro J, Poussin K, Franconi A, Couchy G, Morcrette G, et al. Genomic profiling of hepatocellular adenomas reveals recurrent FRK-activating mutations and the mechanisms of malignant transformation. Cancer Cell. 2014;25:428–41.
Article
CAS
PubMed
Google Scholar
Anoosha P, Huang LT, Sakthivel R, Karunagaran D, Gromiha MM. Discrimination of driver and passenger mutations in epidermal growth factor receptor in cancer. Mutat Res. 2015;780:24–34.
Article
CAS
PubMed
Google Scholar
Anoosha P, Sakthivel R, Michael Gromiha M. Exploring preferred amino acid mutations in cancer genes: Applications to identify potential drug targets. Biochim Biophys Acta. 1862;2016:155–65.
Google Scholar
Faraone D, Aguzzi MS, Ragone G, Russo K, Capogrossi MC, Facchiano A. Heterodimerization of FGF-receptor 1 and PDGF-receptor-alpha: a novel mechanism underlying the inhibitory effect of PDGF-BB on FGF-2 in human cells. Blood. 2006;107:1896–902.
Article
CAS
PubMed
Google Scholar
Citri A, Skaria KB, Yarden Y. The deaf and the dumb: the biology of ErbB-2 and ErbB-3. Exp Cell Res. 2003;284:54–65.
Article
CAS
PubMed
Google Scholar
Cudmore MJ, Hewett PW, Ahmad S, Wang KQ, Cai M, Al-Ani B, Fujisawa T, Ma B, Sissaoui S, Ramma W, et al. The role of heterodimerization between VEGFR-1 and VEGFR-2 in the regulation of endothelial cell homeostasis. Nat Commun. 2012;3:972.
Article
PubMed
Google Scholar
Tian E, Borset M, Sawyer JR, Brede G, Vatsveen TK, Hov H, Waage A, Barlogie B, Shaughnessy JD, Jr., Epstein J, Sundan A. Allelic mutations in noncoding genomic sequences construct novel transcription factor binding sites that promote gene overexpression. Genes Chromosomes Cancer. 2015;54:692–701.
Article
CAS
PubMed
Google Scholar
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;46:1258–63.
Article
CAS
PubMed
Google Scholar
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.
Article
CAS
PubMed
PubMed Central
Google Scholar
Petersen BS, Spehlmann ME, Raedler A, Stade B, Thomsen I, Rabionet R, Rosenstiel P, Schreiber S, Franke A. Whole genome and exome sequencing of monozygotic twins discordant for Crohn's disease. BMC Genomics. 2014;15:564.
Article
PubMed
PubMed Central
Google Scholar
Hunt KA, Mistry V, Bockett NA, Ahmad T, Ban M, Barker JN, Barrett JC, Blackburn H, Brand O, Burren O, et al. Negligible impact of rare autoimmune-locus coding-region variants on missing heritability. Nature. 2013;498:232–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yuen RK, Thiruvahindrapuram B, Merico D, Walker S, Tammimies K, Hoang N, Chrysler C, Nalpathamkalam T, Pellecchia G, Liu Y, et al. Whole-genome sequencing of quartet families with autism spectrum disorder. Nat Med. 2015;21:185–91.
Article
CAS
PubMed
Google Scholar
Yang Y, Muzny DM, Reid JG, Bainbridge MN, Willis A, Ward PA, Braxton A, Beuten J, Xia F, Niu Z, et al. Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med. 2013;369:1502–11.
Article
CAS
PubMed
PubMed Central
Google Scholar
The UK10K project identifies rare variants in health and disease. Nature. 2015.
Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, et al. The UCSC Genome Browser database: 2014 update. Nucleic Acids Res. 2014;42:D764–770.
Article
CAS
PubMed
PubMed Central
Google Scholar
Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, Rahman N, Stratton MR. A census of human cancer genes. Nat Rev Cancer. 2004;4:177–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 2010;38:D355–360.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 2005;33:D514–517.
Article
CAS
PubMed
PubMed Central
Google Scholar
Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27:573–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dinkel H, Chica C, Via A, Gould CM, Jensen LJ, Gibson TJ, Diella F. Phospho.ELM: a database of phosphorylation sites--update 2011. Nucleic Acids Res. 2011;39:D261–267.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dosztanyi Z, Csizmok V, Tompa P, Simon I. The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. J Mol Biol. 2005;347:827–39.
Article
CAS
PubMed
Google Scholar
Dosztanyi Z, Csizmok V, Tompa P, Simon I. IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics. 2005;21:3433–4.
Article
CAS
PubMed
Google Scholar
Dosztanyi Z, Meszaros B, Simon I. ANCHOR: web server for predicting protein binding regions in disordered proteins. Bioinformatics. 2009;25:2745–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Meszaros B, Simon I, Dosztanyi Z. Prediction of protein binding regions in disordered proteins. PLoS Comput Biol. 2009;5:e1000376.
Article
PubMed
PubMed Central
Google Scholar