Babur, O.Dogrusoz, U.Çakır, M.Aksoy, B. A.Schultz, N.Sander, C.Demir, E.2016-02-082016-02-0820141471-2164http://hdl.handle.net/11693/25558Background: 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.EnglishGenomic data analysisPathway informaticsAutomationBiologyComputer graphicsComputer programGene expressionGenomicsInformation processingIntermethod comparisonMolecular geneticsBreast tumorEndometrial neoplasmsSoftwareArticle10.1186/1471-2164-15-642