Visualizing multidimensional cancer genomics data

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• dc.contributor.author Schroeder, Michael Philipp, 1986-ca
• dc.contributor.author González-Pérez, Abelca
• dc.contributor.author López Bigas, Núriaca
• dc.date.accessioned 2015-03-16T08:16:18Z
• dc.date.available 2015-03-16T08:16:18Z
• dc.date.issued 2013ca
• dc.description.abstract Cancer genomics projects employ high-throughput technologies to identify the complete catalog of somatic alterations that characterize the genome, transcriptome and epigenome of cohorts of tumor samples. Examples include projects carried out by the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). A crucial step in the extraction of knowledge from the data is the exploration by experts of the different alterations, as well as the multiple relationships between them. To that end, the use of intuitive visualization tools that can integrate different types of alterations with clinical data is essential to the field of cancer genomics. Here, we review effective and common visualization techniques for exploring oncogenomics data and discuss a selection of tools that allow researchers to effectively visualize multidimensional oncogenomics datasets. The review covers visualization methods employed by tools such as Circos, Gitools, the Integrative Genomics Viewer, Cytoscape, Savant Genome Browser, StratomeX and platforms such as cBio Cancer Genomics Portal, IntOGen, the UCSC Cancer Genomics Browser, the Regulome Explorer and the Cancer Genome Workbench.en
• dc.description.sponsorship We acknowledge funding from the Spanish Ministry of Science and Technology (grant number SAF009-06954 and FPI fellowship assigned to MPS), and from the Spanish National Institute of Bioinformatics (INB)en
• dc.format.mimetype application/pdfca
• dc.identifier.citation Schroeder MP, Gonzalez-Perez A, Lopez-Bigas N. Visualizing multidimensional cancer genomics data. Genome Medicine. 2013; 5: 9. DOI 10.1186/gm413ca
• dc.identifier.doi http://dx.doi.org/10.1186/gm413
• dc.identifier.issn 1756-994Xca
• dc.identifier.uri http://hdl.handle.net/10230/23185
• dc.language.iso engca
• dc.publisher BioMed Centralca
• dc.relation.ispartof Genome Medicine. 2013; 5: 9
• dc.rights © 2013 BioMed Central Ltdca
• dc.rights.accessRights info:eu-repo/semantics/openAccessca
• dc.subject.other Càncer -- Aspectes genèticsca
• dc.title Visualizing multidimensional cancer genomics dataca
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersionca