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dc.contributor.authorBabur, O.en_US
dc.contributor.authorDogrusoz, U.en_US
dc.contributor.authorÇakır, M.en_US
dc.contributor.authorAksoy, B. A.en_US
dc.contributor.authorSchultz, N.en_US
dc.contributor.authorSander, C.en_US
dc.contributor.authorDemir, E.en_US
dc.date.accessioned2016-02-08T10:46:48Z
dc.date.available2016-02-08T10:46:48Z
dc.date.issued2014en_US
dc.identifier.issn1471-2164
dc.identifier.urihttp://hdl.handle.net/11693/25558
dc.description.abstractBackground: Dynamic visual exploration of detailed pathway information can help researchers digest and interpret complex mechanisms and genomic datasets.Results: ChiBE is a free, open-source software tool for visualizing, querying, and analyzing human biological pathways in BioPAX format. The recently released version 2 can search for neighborhoods, paths between molecules, and common regulators/targets of molecules, on large integrated cellular networks in the Pathway Commons database as well as in local BioPAX models. Resulting networks can be automatically laid out for visualization using a graphically rich, process-centric notation. Profiling data from the cBioPortal for Cancer Genomics and expression data from the Gene Expression Omnibus can be overlaid on these networks.Conclusions: ChiBE's new capabilities are organized around a genomics-oriented workflow and offer a unique comprehensive pathway analysis solution for genomics researchers. The software is freely available at http://code.google.com/p/chibe. © 2014 Babur et al.; licensee BioMed Central Ltd.en_US
dc.language.isoEnglishen_US
dc.source.titleBMC Genomicsen_US
dc.relation.isversionofhttp://dx.doi.org/10.1186/1471-2164-15-642en_US
dc.subjectGenomic data analysisen_US
dc.subjectPathway informaticsen_US
dc.subjectAutomationen_US
dc.subjectBiologyen_US
dc.subjectComputer graphicsen_US
dc.subjectComputer programen_US
dc.subjectGene expressionen_US
dc.subjectGenomicsen_US
dc.subjectInformation processingen_US
dc.subjectIntermethod comparisonen_US
dc.subjectMolecular geneticsen_US
dc.subjectBreast tumoren_US
dc.subjectEndometrial neoplasmsen_US
dc.subjectSoftwareen_US
dc.titleIntegrating biological pathways and genomic profiles with ChiBE 2en_US
dc.typeArticleen_US
dc.departmentDepartment of Computer Engineering
dc.citation.spage1en_US
dc.citation.epage9en_US
dc.citation.volumeNumber15en_US
dc.citation.issueNumber642en_US
dc.identifier.doi10.1186/1471-2164-15-642en_US
dc.publisherBioMed Central Ltd.en_US


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