Integrating biological pathways and genomic profiles with ChiBE 2

Özgün Babur, Ugur Dogrusoz, Merve C¸akir, Bülent A. Aksoy, Nikolaus Schultz, Chris Sander, Emek Demir

Research output: Contribution to journalArticlepeer-review

22 Scopus citations


Background: 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

Original languageEnglish (US)
Article number642
JournalBMC Genomics
Issue number1
StatePublished - Aug 3 2014
Externally publishedYes


  • Genomic data analysis
  • Pathway informatics

ASJC Scopus subject areas

  • Biotechnology
  • Genetics


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