TY - JOUR PY - 2010 DA - 2010// TI - International network of cancer genome projects JO - Nature VL - 464 UR - https://doi.org/10.1038/nature08987 DO - 10.1038/nature08987 ID - ref1 ER - TY - JOUR AU - Tomczak, K. AU - Czerwińska, P. AU - Wiznerowicz, M. PY - 2015 DA - 2015// TI - The Cancer genome atlas (TCGA): an immeasurable source of knowledge JO - Contemp Oncol VL - 19 ID - Tomczak2015 ER - TY - JOUR AU - Nakagawa, H. AU - Fujita, M. PY - 2018 DA - 2018// TI - Whole genome sequencing analysis for cancer genomics and precision medicine JO - Cancer Sci VL - 109 UR - https://doi.org/10.1111/cas.13505 DO - 10.1111/cas.13505 ID - Nakagawa2018 ER - TY - STD TI - Poulos RC, Wong JW. Finding cancer driver mutations in the era of big data research. Biophys Rev. 2018;10:1–9. ID - ref4 ER - TY - JOUR AU - Weinstein, J. N. AU - Collisson, E. A. AU - Mills, G. B. AU - Shaw, K. R. AU - Ozenberger, B. A. AU - Ellrott, K. AU - Shmulevich, I. AU - Sander, C. AU - Stuart, J. M. PY - 2013 DA - 2013// TI - The Cancer Genome Atlas Pan-Cancer analysis project JO - Nat Genet VL - 45 UR - https://doi.org/10.1038/ng.2764 DO - 10.1038/ng.2764 ID - Weinstein2013 ER - TY - JOUR AU - Bailey, M. H. AU - Tokheim, C. AU - Porta-Pardo, E. AU - Sengupta, S. AU - Bertrand, D. AU - Weerasinghe, A. AU - Colaprico, A. AU - Wendl, M. C. AU - Kim, J. AU - Reardon, B. PY - 2018 DA - 2018// TI - Comprehensive characterization of cancer driver genes and mutations JO - Cell VL - 173 UR - https://doi.org/10.1016/j.cell.2018.02.060 DO - 10.1016/j.cell.2018.02.060 ID - Bailey2018 ER - TY - JOUR AU - Hutter, C. AU - Zenklusen, J. C. PY - 2018 DA - 2018// TI - The Cancer genome atlas: creating lasting value beyond its data JO - Cell VL - 173 UR - https://doi.org/10.1016/j.cell.2018.03.042 DO - 10.1016/j.cell.2018.03.042 ID - Hutter2018 ER - TY - JOUR AU - Syed, A. S. AU - D'Antonio, M. AU - Ciccarelli, F. D. PY - 2010 DA - 2010// TI - Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes JO - Nucleic Acids Res VL - 38 UR - https://doi.org/10.1093/nar/gkp957 DO - 10.1093/nar/gkp957 ID - Syed2010 ER - TY - JOUR AU - D'Antonio, M. AU - Pendino, V. AU - Sinha, S. AU - Ciccarelli, F. D. PY - 2012 DA - 2012// TI - Network of Cancer Genes (NCG 3.0): integration and analysis of genetic and network properties of cancer genes JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr952 DO - 10.1093/nar/gkr952 ID - D'Antonio2012 ER - TY - JOUR AU - An, O. AU - Pendino, V. AU - D’Antonio, M. AU - Ratti, E. AU - Gentilini, M. AU - Ciccarelli, F. D. PY - 2014 DA - 2014// TI - NCG 4.0: the network of cancer genes in the era of massive mutational screenings of cancer genomes JO - Database VL - 2014 UR - https://doi.org/10.1093/database/bau015 DO - 10.1093/database/bau015 ID - An2014 ER - TY - JOUR AU - An, O. AU - Dall'Olio, G. M. AU - Mourikis, T. P. AU - Ciccarelli, F. D. PY - 2016 DA - 2016// TI - NCG 5.0: updates of a manually curated repository of cancer genes and associated properties from cancer mutational screenings JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkv1123 DO - 10.1093/nar/gkv1123 ID - An2016 ER - TY - JOUR AU - Ciccarelli, F. D. PY - 2010 DA - 2010// TI - The (r)evolution of cancer genetics JO - BMC Biol VL - 8 UR - https://doi.org/10.1186/1741-7007-8-74 DO - 10.1186/1741-7007-8-74 ID - Ciccarelli2010 ER - TY - JOUR AU - Forbes, S. A. AU - Beare, D. AU - Boutselakis, H. AU - Bamford, S. AU - Bindal, N. AU - Tate, J. AU - Cole, C. G. AU - Ward, S. AU - Dawson, E. AU - Ponting, L. PY - 2017 DA - 2017// TI - COSMIC: somatic cancer genetics at high-resolution JO - Nucleic Acids Res VL - 45 UR - https://doi.org/10.1093/nar/gkw1121 DO - 10.1093/nar/gkw1121 ID - Forbes2017 ER - TY - JOUR AU - Ainscough, B. J. AU - Griffith, M. AU - Coffman, A. C. AU - Wagner, A. H. AU - Kunisaki, J. AU - Choudhary, M. N. AU - McMichael, J. F. AU - Fulton, R. S. AU - Wilson, R. K. AU - Griffith, O. L. AU - Mardis, E. R. PY - 2016 DA - 2016// TI - DoCM: a database of curated mutations in cancer JO - Nat Methods VL - 13 UR - https://doi.org/10.1038/nmeth.4000 DO - 10.1038/nmeth.4000 ID - Ainscough2016 ER - TY - JOUR AU - Chung, I. F. AU - Chen, C. Y. AU - Su, S. C. AU - Li, C. Y. AU - Wu, K. J. AU - Wang, H. W. AU - Cheng, W. C. PY - 2016 DA - 2016// TI - DriverDBv2: a database for human cancer driver gene research JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkv1314 DO - 10.1093/nar/gkv1314 ID - Chung2016 ER - TY - JOUR AU - Tamborero, D. AU - Rubio-Perez, C. AU - Deu-Pons, J. AU - Schroeder, M. P. AU - Vivancos, A. AU - Rovira, A. AU - Tusquets, I. AU - Albanell, J. AU - Rodon, J. AU - Tabernero, J. PY - 2018 DA - 2018// TI - Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations JO - Genome Med VL - 10 UR - https://doi.org/10.1186/s13073-018-0531-8 DO - 10.1186/s13073-018-0531-8 ID - Tamborero2018 ER - TY - STD TI - Chakravarty D, Gao J, Phillips SM, Kundra R, Zhang H, Wang J, Rudolph JE, Yaeger R, Soumerai T, Nissan MH, et al. OncoKB: a precision oncology Knowledge Base. JCO Precis Oncol. 2017;1:1–16. ID - ref17 ER - TY - JOUR AU - Cerami, E. AU - Gao, J. AU - Dogrusoz, U. AU - Gross, B. E. AU - Sumer, S. O. AU - Aksoy, B. A. AU - Jacobsen, A. AU - Byrne, C. J. AU - Heuer, M. L. AU - Larsson, E. PY - 2012 DA - 2012// TI - The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data JO - Cancer Discov VL - 2 UR - https://doi.org/10.1158/2159-8290.CD-12-0095 DO - 10.1158/2159-8290.CD-12-0095 ID - Cerami2012 ER - TY - JOUR AU - Futreal, P. A. AU - Coin, L. AU - Marshall, M. AU - Down, T. AU - Hubbard, T. AU - Wooster, R. AU - Rahman, N. AU - Stratton, M. R. PY - 2004 DA - 2004// TI - A census of human cancer genes JO - Nat Rev Cancer VL - 4 UR - https://doi.org/10.1038/nrc1299 DO - 10.1038/nrc1299 ID - Futreal2004 ER - TY - JOUR AU - Liu, Y. AU - Sun, J. AU - Zhao, M. PY - 2017 DA - 2017// TI - ONGene: a literature-based database for human oncogenes JO - J Genet Genomics VL - 44 UR - https://doi.org/10.1016/j.jgg.2016.12.004 DO - 10.1016/j.jgg.2016.12.004 ID - Liu2017 ER - TY - JOUR AU - Zhao, M. AU - Kim, P. AU - Mitra, R. AU - Zhao, J. AU - Zhao, Z. PY - 2016 DA - 2016// TI - TSGene 2.0: an updated literature-based knowledgebase for tumor suppressor genes JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkv1268 DO - 10.1093/nar/gkv1268 ID - Zhao2016 ER - TY - STD TI - Agarwal R, Kumar B, Jayadev M, Raghav D, Singh A. CoReCG: a comprehensive database of genes associated with colon-rectal cancer. Database (Oxford). 2016;2016:1-9. ID - ref22 ER - TY - JOUR AU - Andres-Leon, E. AU - Cases, I. AU - Alonso, S. AU - Rojas, A. M. PY - 2017 DA - 2017// TI - Novel miRNA-mRNA interactions conserved in essential cancer pathways JO - Sci Rep VL - 7 UR - https://doi.org/10.1038/srep46101 DO - 10.1038/srep46101 ID - Andres-Leon2017 ER - TY - JOUR AU - Jakel, C. AU - Bergmann, F. AU - Toth, R. AU - Assenov, Y. AU - Duin, D. AU - Strobel, O. AU - Hank, T. AU - Kloppel, G. AU - Dorrell, C. AU - Grompe, M. PY - 2017 DA - 2017// TI - Genome-wide genetic and epigenetic analyses of pancreatic acinar cell carcinomas reveal aberrations in genome stability JO - Nat Commun VL - 8 UR - https://doi.org/10.1038/s41467-017-01118-x DO - 10.1038/s41467-017-01118-x ID - Jakel2017 ER - TY - JOUR AU - Woollard, W. J. AU - Pullabhatla, V. AU - Lorenc, A. AU - Patel, V. M. AU - Butler, R. M. AU - Bayega, A. AU - Begum, N. AU - Bakr, F. AU - Dedhia, K. AU - Fisher, J. PY - 2016 DA - 2016// TI - Candidate driver genes involved in genome maintenance and DNA repair in Sezary syndrome JO - Blood VL - 127 UR - https://doi.org/10.1182/blood-2016-02-699843 DO - 10.1182/blood-2016-02-699843 ID - Woollard2016 ER - TY - JOUR AU - Xiong, D. AU - Pan, J. AU - Zhang, Q. AU - Szabo, E. AU - Miller, M. S. AU - Lubet, R. A. AU - You, M. AU - Wang, Y. PY - 2017 DA - 2017// TI - Bronchial airway gene expression signatures in mouse lung squamous cell carcinoma and their modulation by cancer chemopreventive agents JO - Oncotarget VL - 8 ID - Xiong2017 ER - TY - JOUR AU - Chiu, H. S. AU - Somvanshi, S. AU - Patel, E. AU - Chen, T. W. AU - Singh, V. P. AU - Zorman, B. AU - Patil, S. L. AU - Pan, Y. AU - Chatterjee, S. S. PY - 2018 DA - 2018// TI - Pan-Cancer analysis of lncRNA regulation supports their targeting of cancer genes in each tumor context JO - Cell Rep VL - 23 UR - https://doi.org/10.1016/j.celrep.2018.03.064 DO - 10.1016/j.celrep.2018.03.064 ID - Chiu2018 ER - TY - JOUR AU - Rosanova, A. AU - Colliva, A. AU - Osella, M. AU - Caselle, M. PY - 2017 DA - 2017// TI - Modelling the evolution of transcription factor binding preferences in complex eukaryotes JO - Sci Rep VL - 7 UR - https://doi.org/10.1038/s41598-017-07761-0 DO - 10.1038/s41598-017-07761-0 ID - Rosanova2017 ER - TY - JOUR AU - Kanehisa, M. AU - Furumichi, M. AU - Tanabe, M. AU - Sato, Y. AU - Morishima, K. PY - 2016 DA - 2016// TI - KEGG: new perspectives on genomes, pathways, diseases and drugs JO - Nucleic Acids Res VL - 45 UR - https://doi.org/10.1093/nar/gkw1092 DO - 10.1093/nar/gkw1092 ID - Kanehisa2016 ER - TY - JOUR AU - Fabregat, A. AU - Jupe, S. AU - Matthews, L. AU - Sidiropoulos, K. AU - Gillespie, M. AU - Garapati, P. AU - Haw, R. AU - Jassal, B. AU - Korninger, F. AU - May, B. PY - 2018 DA - 2018// TI - The Reactome pathway knowledgebase JO - Nucleic Acids Res VL - 46 UR - https://doi.org/10.1093/nar/gkx1132 DO - 10.1093/nar/gkx1132 ID - Fabregat2018 ER - TY - JOUR AU - Nishimura, D. PY - 2001 DA - 2001// TI - BioCarta JO - Biotech Software Intern Rep VL - 2 UR - https://doi.org/10.1089/152791601750294344 DO - 10.1089/152791601750294344 ID - Nishimura2001 ER - TY - STD TI - Elmasri R, Navathe S. Fundamentals of database systems. Boston: Addison-Wesley Publishing Company; 2010. ID - ref32 ER - TY - JOUR AU - O'Leary, N. A. AU - Wright, M. W. AU - Brister, J. R. AU - Ciufo, S. AU - Haddad, D. AU - McVeigh, R. AU - Rajput, B. AU - Robbertse, B. AU - Smith-White, B. AU - Ako-Adjei, D. PY - 2016 DA - 2016// TI - Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkv1189 DO - 10.1093/nar/gkv1189 ID - O'Leary2016 ER - TY - JOUR AU - Kent, W. J. PY - 2002 DA - 2002// TI - BLAT--the BLAST-like alignment tool JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.229202 DO - 10.1101/gr.229202 ID - Kent2002 ER - TY - JOUR AU - Rambaldi, D. AU - Giorgi, F. M. AU - Capuani, F. AU - Ciliberto, A. AU - Ciccarelli, F. D. PY - 2008 DA - 2008// TI - Low duplicability and network fragility of cancer genes JO - Trends Genet VL - 24 UR - https://doi.org/10.1016/j.tig.2008.06.003 DO - 10.1016/j.tig.2008.06.003 ID - Rambaldi2008 ER - TY - JOUR AU - Huerta-Cepas, J. AU - Szklarczyk, D. AU - Forslund, K. AU - Cook, H. AU - Heller, D. AU - Walter, M. C. AU - Rattei, T. AU - Mende, D. R. AU - Sunagawa, S. AU - Kuhn, M. PY - 2015 DA - 2015// TI - eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkv1248 DO - 10.1093/nar/gkv1248 ID - Huerta-Cepas2015 ER - TY - JOUR AU - D’Antonio, M. AU - Ciccarelli, F. D. PY - 2011 DA - 2011// TI - Modification of gene duplicability during the evolution of protein interaction network JO - PLoS Comput Biol VL - 7 UR - https://doi.org/10.1371/journal.pcbi.1002029 DO - 10.1371/journal.pcbi.1002029 ID - D’Antonio2011 ER - TY - JOUR AU - Uhlen, M. AU - Fagerberg, L. AU - Hallstrom, B. M. AU - Lindskog, C. AU - Oksvold, P. AU - Mardinoglu, A. AU - Sivertsson, A. AU - Kampf, C. AU - Sjostedt, E. AU - Asplund, A. PY - 2015 DA - 2015// TI - Proteomics. Tissue-based map of the human proteome JO - Science VL - 347 UR - https://doi.org/10.1126/science.1260419 DO - 10.1126/science.1260419 ID - Uhlen2015 ER - TY - JOUR AU - Lonsdale, J. AU - Thomas, J. AU - Salvatore, M. AU - Phillips, R. AU - Lo, E. AU - Shad, S. AU - Hasz, R. AU - Walters, G. AU - Garcia, F. AU - Young, N. PY - 2013 DA - 2013// TI - The genotype-tissue expression (GTEx) project JO - Nat Genet VL - 45 UR - https://doi.org/10.1038/ng.2653 DO - 10.1038/ng.2653 ID - Lonsdale2013 ER - TY - STD TI - Cancer Cell Line Encyclopedia Consortium, Genomics of Drug Sensitivity in Cancer Consortium: Pharmacogenomic agreement between two cancer cell line data sets. Nature 2015, 528:84. ID - ref40 ER - TY - JOUR AU - Klijn, C. AU - Durinck, S. AU - Stawiski, E. W. AU - Haverty, P. M. AU - Jiang, Z. AU - Liu, H. AU - Degenhardt, J. AU - Mayba, O. AU - Gnad, F. AU - Liu, J. PY - 2015 DA - 2015// TI - A comprehensive transcriptional portrait of human cancer cell lines JO - Nat Biotechnol VL - 33 UR - https://doi.org/10.1038/nbt.3080 DO - 10.1038/nbt.3080 ID - Klijn2015 ER - TY - JOUR AU - Lenoir, W. F. AU - Lim, T. L. AU - Hart, T. PY - 2018 DA - 2018// TI - PICKLES: the database of pooled in-vitro CRISPR knockout library essentiality screens JO - Nucleic Acids Res VL - 46 UR - https://doi.org/10.1093/nar/gkx993 DO - 10.1093/nar/gkx993 ID - Lenoir2018 ER - TY - JOUR AU - Chen, W. H. AU - Lu, G. AU - Chen, X. AU - Zhao, X. M. AU - Bork, P. PY - 2017 DA - 2017// TI - OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines JO - Nucleic Acids Res VL - 45 UR - https://doi.org/10.1093/nar/gkw1013 DO - 10.1093/nar/gkw1013 ID - Chen2017 ER - TY - JOUR AU - Hart, T. AU - Tong, A. H. Y. AU - Chan, K. AU - Leeuwen, J. AU - Seetharaman, A. AU - Aregger, M. AU - Chandrashekhar, M. AU - Hustedt, N. AU - Seth, S. AU - Noonan, A. PY - 2017 DA - 2017// TI - Evaluation and design of genome-wide CRISPR/SpCas9 knockout screens JO - G3 (Bethesda) VL - 7 UR - https://doi.org/10.1534/g3.117.041277 DO - 10.1534/g3.117.041277 ID - Hart2017 ER - TY - JOUR AU - Chatr-Aryamontri, A. AU - Oughtred, R. AU - Boucher, L. AU - Rust, J. AU - Chang, C. AU - Kolas, N. K. AU - O'Donnell, L. AU - Oster, S. AU - Theesfeld, C. AU - Sellam, A. PY - 2017 DA - 2017// TI - The BioGRID interaction database: 2017 update JO - Nucleic Acids Res VL - 45 UR - https://doi.org/10.1093/nar/gkw1102 DO - 10.1093/nar/gkw1102 ID - Chatr-Aryamontri2017 ER - TY - JOUR AU - Orchard, S. AU - Ammari, M. AU - Aranda, B. AU - Breuza, L. AU - Briganti, L. AU - Broackes-Carter, F. AU - Campbell, N. H. AU - Chavali, G. AU - Chen, C. AU - del-Toro, N. PY - 2014 DA - 2014// TI - The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1115 DO - 10.1093/nar/gkt1115 ID - Orchard2014 ER - TY - JOUR AU - Salwinski, L. AU - Miller, C. S. AU - Smith, A. J. AU - Pettit, F. K. AU - Bowie, J. U. AU - Eisenberg, D. PY - 2004 DA - 2004// TI - The database of interacting proteins: 2004 update JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh086 DO - 10.1093/nar/gkh086 ID - Salwinski2004 ER - TY - JOUR AU - Keshava Prasad, T. S. AU - Goel, R. AU - Kandasamy, K. AU - Keerthikumar, S. AU - Kumar, S. AU - Mathivanan, S. AU - Telikicherla, D. AU - Raju, R. AU - Shafreen, B. AU - Venugopal, A. PY - 2009 DA - 2009// TI - Human protein reference database--2009 update JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkn892 DO - 10.1093/nar/gkn892 ID - Keshava Prasad2009 ER - TY - JOUR AU - Ruepp, A. AU - Waegele, B. AU - Lechner, M. AU - Brauner, B. AU - Dunger-Kaltenbach, I. AU - Fobo, G. AU - Frishman, G. AU - Montrone, C. AU - Mewes, H. W. PY - 2010 DA - 2010// TI - CORUM: the comprehensive resource of mammalian protein complexes--2009 JO - Nucleic Acids Res VL - 38 UR - https://doi.org/10.1093/nar/gkp914 DO - 10.1093/nar/gkp914 ID - Ruepp2010 ER - TY - JOUR AU - Chou, C. -. H. AU - Shrestha, S. AU - Yang, C. -. D. AU - Chang, N. -. W. AU - Lin, Y. -. L. AU - Liao, K. -. W. AU - Huang, W. -. C. AU - Sun, T. -. H. AU - Tu, S. -. J. AU - Lee, W. -. H. PY - 2017 DA - 2017// TI - miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions JO - Nucleic Acids Res VL - 46 UR - https://doi.org/10.1093/nar/gkx1067 DO - 10.1093/nar/gkx1067 ID - Chou2017 ER - TY - JOUR AU - Xiao, F. AU - Zuo, Z. AU - Cai, G. AU - Kang, S. AU - Gao, X. AU - Li, T. PY - 2009 DA - 2009// TI - miRecords: an integrated resource for microRNA-target interactions JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkn851 DO - 10.1093/nar/gkn851 ID - Xiao2009 ER - TY - JOUR AU - Schaefer, C. AU - Grouse, L. AU - Buetow, K. AU - Strausberg, R. L. PY - 2001 DA - 2001// TI - A new cancer genome anatomy project web resource for the community JO - Cancer J VL - 7 ID - Schaefer2001 ER - TY - JOUR AU - Vogelstein, B. AU - Papadopoulos, N. AU - Velculescu, V. E. AU - Zhou, S. AU - Diaz, L. A. AU - Kinzler, K. W. PY - 2013 DA - 2013// TI - Cancer genome landscapes JO - Science VL - 339 UR - https://doi.org/10.1126/science.1235122 DO - 10.1126/science.1235122 ID - Vogelstein2013 ER - TY - JOUR AU - Dulak, A. M. AU - Stojanov, P. AU - Peng, S. AU - Lawrence, M. S. AU - Fox, C. AU - Stewart, C. AU - Bandla, S. AU - Imamura, Y. AU - Schumacher, S. E. AU - Shefler, E. PY - 2013 DA - 2013// TI - Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity JO - Nat Genet VL - 45 UR - https://doi.org/10.1038/ng.2591 DO - 10.1038/ng.2591 ID - Dulak2013 ER - TY - JOUR AU - Lawrence, M. S. AU - Stojanov, P. AU - Polak, P. AU - Kryukov, G. V. AU - Cibulskis, K. AU - Sivachenko, A. AU - Carter, S. L. AU - Stewart, C. AU - Mermel, C. H. AU - Roberts, S. A. PY - 2013 DA - 2013// TI - Mutational heterogeneity in cancer and the search for new cancer-associated genes JO - Nature VL - 499 UR - https://doi.org/10.1038/nature12213 DO - 10.1038/nature12213 ID - Lawrence2013 ER - TY - JOUR AU - Dees, N. D. AU - Zhang, Q. AU - Kandoth, C. AU - Wendl, M. C. AU - Schierding, W. AU - Koboldt, D. C. AU - Mooney, T. B. AU - Callaway, M. B. AU - Dooling, D. AU - Mardis, E. R. PY - 2012 DA - 2012// TI - MuSiC: identifying mutational significance in cancer genomes JO - Genome Res VL - 22 UR - https://doi.org/10.1101/gr.134635.111 DO - 10.1101/gr.134635.111 ID - Dees2012 ER - TY - JOUR AU - Hao, D. AU - Wang, L. AU - Di, L. J. PY - 2016 DA - 2016// TI - Distinct mutation accumulation rates among tissues determine the variation in cancer risk JO - Sci Rep VL - 6 UR - https://doi.org/10.1038/srep19458 DO - 10.1038/srep19458 ID - Hao2016 ER - TY - JOUR AU - Chu, X. -. Y. AU - Jiang, L. -. H. AU - Zhou, X. -. H. AU - Cui, Z. -. J. AU - Zhang, H. -. Y. PY - 2017 DA - 2017// TI - Evolutionary origins of cancer driver genes and implications for cancer prognosis JO - Genes VL - 8 UR - https://doi.org/10.3390/genes8070182 DO - 10.3390/genes8070182 ID - Chu2017 ER - TY - JOUR AU - Domazet-Loso, T. AU - Tautz, D. PY - 2010 DA - 2010// TI - Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa JO - BMC Biol VL - 8 UR - https://doi.org/10.1186/1741-7007-8-66 DO - 10.1186/1741-7007-8-66 ID - Domazet-Loso2010 ER - TY - JOUR AU - Li, Y. AU - Li, L. AU - Wang, Z. AU - Pan, T. AU - Sahni, N. AU - Jin, X. AU - Wang, G. AU - Li, J. AU - Zheng, X. AU - Zhang, Y. PY - 2018 DA - 2018// TI - LncMAP: Pan-cancer atlas of long noncoding RNA-mediated transcriptional network perturbations JO - Nucleic Acids Res VL - 46 UR - https://doi.org/10.1093/nar/gkx1311 DO - 10.1093/nar/gkx1311 ID - Li2018 ER - TY - JOUR AU - D’Antonio, M. AU - Ciccarelli, F. D. PY - 2013 DA - 2013// TI - Integrated analysis of recurrent properties of cancer genes to identify novel drivers JO - Genome Biol VL - 14 UR - https://doi.org/10.1186/gb-2013-14-5-r52 DO - 10.1186/gb-2013-14-5-r52 ID - D’Antonio2013 ER - TY - STD TI - Nishimura D: BioCarta.https://cgap.nci.nih.gov/Pathways/BioCarta_Pathways. Accessed 16 Apr 2018. UR - https://cgap.nci.nih.gov/Pathways/BioCarta_Pathways ID - ref62 ER - TY - STD TI - Chatr-Aryamontri A, Oughtred R, Boucher L, Rust J, Chang C, Kolas NK, O'Donnell L, Oster S, Theesfeld C, Sellam A, et al: Biological General Repository for Interaction Datasets (BioGRID). re3data (https://doi.org/10.17616/r34c7g). Accessed 19 Feb 2018. ID - ref63 ER - TY - STD TI - Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehar J, Kryukov GV, Sonkin D, et al: The Cancer Cell Line Encyclopedia. https://portals.broadinstitute.org/ccle. Accessed 23 Mar 2018. UR - https://portals.broadinstitute.org/ccle ID - ref64 ER - TY - STD TI - Forbes SA, Beare D, Boutselakis H, Bamford S, Bindal N, Tate J, Cole CG, Ward S, Dawson E, Ponting L, et al: COSMIC Cancer Cell Line Project.https://cancer.sanger.ac.uk/cell_lines. Accessed 23 Mar 2018. UR - https://cancer.sanger.ac.uk/cell_lines ID - ref65 ER - TY - STD TI - Ruepp A, Waegele B, Lechner M, Brauner B, Dunger-Kaltenbach I, Fobo G, Frishman G, Montrone C, Mewes HW: The Comprehensive Resource of Mammalian protein complexes (CORUM). re3data (https://doi.org/10.17616/r3nk8k). Accessed 19 Feb 2018. ID - ref66 ER - TY - STD TI - Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D: Database of Interacting Proteins (DIP). re3data (https://doi.org/10.17616/r3vg8d). Accessed 19 Feb 2018. ID - ref67 ER - TY - STD TI - Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M. eggNOG 4.5.1. FAIRsharing. https://doi.org/10.25504/fairsharing.j1wj7d. Accessed 16 Apr 2018. ID - ref68 ER - TY - STD TI - Klijn C, Durinck S, Stawiski EW, Haverty PM, Jiang Z, Liu H, Degenhardt J, Mayba O, Gnad F, Liu J, et al: Genentech expression dataset.: EBI Array Express, accession number E-MTAB-2607 (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-2607/). Accessed 23 Mar 2018. UR - https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-2607/ ID - ref69 ER - TY - STD TI - Lonsdale J, Thomas J, Salvatore M, Phillips R, Lo E, Shad S, Hasz R, Walters G, Garcia F, Young N. The genotype-tissue expression (GTEx) project. DataCite. https://doi.org/10.25491/j0aj-4w78. Accessed 23 Mar 2018. ID - ref70 ER - TY - STD TI - Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, et al: The Human Protein Reference Database (HPRD). re3data (https://doi.org/10.17616/r3mk9n). Accessed 19 Feb 2018. ID - ref71 ER - TY - STD TI - Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K: KEGG pathway database http://www.genome.jp/kegg/pathway.html. Accessed 16 Apr 2018. UR - http://www.genome.jp/kegg/pathway.html ID - ref72 ER - TY - STD TI - Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F, Campbell NH, Chavali G, Chen C, del-Toro N, et al: The MIntAct project. re3data (https://doi.org/10.17616/r3qs4r). Accessed 19 Feb 2018. ID - ref73 ER - TY - STD TI - Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T: miRecords v.4.0. http://c1.accurascience.com/miRecords/. Accessed 4 June 2018. UR - http://c1.accurascience.com/miRecords/ ID - ref74 ER - TY - STD TI - Chou C-H, Shrestha S, Yang C-D, Chang N-W, Lin Y-L, Liao K-W, Huang W-C, Sun T-H, Tu S-J, Lee W-H. miRTarBase v.7.0. FAIRsharing. https://doi.org/10.25504/fairsharing.f0bxfg. Accessed 4 June 2018. ID - ref75 ER - TY - STD TI - Chen WH, Lu G, Chen X, Zhao XM, Bork P. Online Gene Essentiality database (OGEE). FAIRsharing. https://doi.org/10.25504/fairsharing.hsy066. Accessed 29 May 2018. ID - ref76 ER - TY - STD TI - Lenoir WF, Lim TL, Hart T. Pooled In-vitro CRISPR Knockout Library Essentiality Screens (PICKLES) http://pickles.hart-lab.org/. Accessed 29 May 2018. UR - http://pickles.hart-lab.org/ ID - ref77 ER - TY - STD TI - Uhlen M, Fagerberg L, Hallstrom BM, Lindskog C, Oksvold P, Mardinoglu A, Sivertsson A, Kampf C, Sjostedt E, Asplund A, et al. The human protein atlas. FAIRsharing. https://doi.org/10.25504/fairsharing.tf6kj8. Accessed 23 Mar 2018. ID - ref78 ER - TY - STD TI - Fabregat A, Jupe S, Matthews L, Sidiropoulos K, Gillespie M, Garapati P, Haw R, Jassal B, Korninger F, May B, et al: Reactome. re3data (https://doi.org/10.17616/r3ts52). Accessed 19 Feb 2018. ID - ref79 ER - TY - STD TI - O'Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, Rajput B, Robbertse B, Smith-White B, Ako-Adjei D, et al: Reference sequence (RefSeq) database release 85. FAIRsharing (https://doi.org/10.25504/FAIRsharing.4jg0qw). Accessed 11 Dec 2017. ID - ref80 ER -