{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T04:16:07Z","timestamp":1773288967013,"version":"3.50.1"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":772,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Several computational methods have been developed to identify cancer drivers genes\u2014genes responsible for cancer development upon specific alterations. These alterations can cause the loss of function (LoF) of the gene product, for instance, in tumor suppressors, or increase or change its activity or function, if it is an oncogene. Distinguishing between these two classes is important to understand tumorigenesis in patients and has implications for therapy decision making. Here, we assess the capacity of multiple gene features related to the pattern of genomic alterations across tumors to distinguish between activating and LoF cancer genes, and we present an automated approach to aid the classification of novel cancer drivers according to their role.<\/jats:p>\n               <jats:p>Result: OncodriveROLE is a machine learning-based approach that classifies driver genes according to their role, using several properties related to the pattern of alterations across tumors. The method shows an accuracy of 0.93 and Matthew's correlation coefficient of 0.84 classifying genes in the Cancer Gene Census. The OncodriveROLE classifier, its results when applied to two lists of predicted cancer drivers and TCGA-derived mutation and copy number features used by the classifier are available at http:\/\/bg.upf.edu\/oncodrive-role.<\/jats:p>\n               <jats:p>Availability and implementation: The R implementation of the OncodriveROLE classifier is available at http:\/\/bg.upf.edu\/oncodrive-role.<\/jats:p>\n               <jats:p>Contact: \u00a0abel.gonzalez@upf.edu or nuria.lopez@upf.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu467","type":"journal-article","created":{"date-parts":[[2014,8,26]],"date-time":"2014-08-26T11:23:57Z","timestamp":1409052237000},"page":"i549-i555","source":"Crossref","is-referenced-by-count":54,"title":["OncodriveROLE classifies cancer driver genes in loss of function and activating mode of action"],"prefix":"10.1093","volume":"30","author":[{"given":"Michael P.","family":"Schroeder","sequence":"first","affiliation":[{"name":"1 Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, E08003 Barcelona and 2Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), E08010 Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carlota","family":"Rubio-Perez","sequence":"additional","affiliation":[{"name":"1 Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, E08003 Barcelona and 2Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), E08010 Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Tamborero","sequence":"additional","affiliation":[{"name":"1 Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, E08003 Barcelona and 2Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), E08010 Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Abel","family":"Gonzalez-Perez","sequence":"additional","affiliation":[{"name":"1 Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, E08003 Barcelona and 2Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), E08010 Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nuria","family":"Lopez-Bigas","sequence":"additional","affiliation":[{"name":"1 Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, E08003 Barcelona and 2Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), E08010 Barcelona, Spain"},{"name":"1 Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, E08003 Barcelona and 2Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), E08010 Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,8,22]]},"reference":[{"key":"2023012711550242400_btu467-B1","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1023\/A:1010933404324","article-title":"Random forests","volume":"45","author":"Breiman","year":"2001","journal-title":"Mach. 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