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OncodriveROLE classifies cancer driver genes in loss of function and activating mode of action

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dc.contributor.author Schroeder, Michael Philipp, 1986-
dc.contributor.author Rubio Pérez, Carlota, 1990-
dc.contributor.author Tamborero Noguera, David
dc.contributor.author González-Pérez, Abel
dc.contributor.author López Bigas, Núria
dc.date.accessioned 2015-09-28T11:47:03Z
dc.date.available 2015-09-28T11:47:03Z
dc.date.issued 2014
dc.identifier.citation Schroeder MP, Rubio-Perez C, Tamborero D, Gonzalez-Perez A, Lopez-Bigas N./nOncodriveROLE classifies cancer driver genes in loss of function and activating mode of action. Bioinformatics. 2014 Sep 1;30(17):549-55. DOI: 10.1093/bioinformatics/btu467
dc.identifier.issn 1367-4803
dc.identifier.uri http://hdl.handle.net/10230/24768
dc.description.abstract MOTIVATION: Several computational methods have been developed to identify cancer drivers genes-genes 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. RESULT: /nOncodriveROLE 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. AVAILABILITY AND IMPLEMENTATION: The R implementation of the OncodriveROLE classifier is available at http://bg.upf.edu/oncodrive-role. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
dc.description.sponsorship This work was supported by the Spanish Ministry of Economy and Competitivity (grant number SAF2012-36199) and the Spanish National Institute of Bioinformatics (INB). M.P.S. and C.R.-P. are supported by FPI fellowships
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Oxford University Press
dc.relation.ispartof Bioinformatics. 2014 Sep 1;30(17):549-55
dc.rights © 2014 Michael Philipp Schroeder et al. Published by Oxford University Press. This is an Open Access article distributed under the terms of a Creative Commons Attribution License
dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
dc.subject.other Intel·ligència artificial
dc.subject.other Tumors
dc.subject.other Oncogens
dc.subject.other Genètica
dc.title OncodriveROLE classifies cancer driver genes in loss of function and activating mode of action
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1093/bioinformatics/btu467
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/SAF2012-36199
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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