Open Access Software

Integrating biological pathways and genomic profiles with ChiBE 2

Özgün Babur1*, Ugur Dogrusoz2, Merve Çakır2, Bülent Arman Aksoy13, Nikolaus Schultz1, Chris Sander1 and Emek Demir1

Author Affiliations

1 Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, Box 460, New York, NY 10065, USA

2 Department of Computer Engineering, Bilkent University, Ankara 06800, Turkey

3 Tri-Institutional Training Program in Computational Biology and Medicine, 1275 York Avenue, New York, NY 10065, USA

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BMC Genomics 2014, 15:642  doi:10.1186/1471-2164-15-642

Published: 3 August 2014



Dynamic visual exploration of detailed pathway information can help researchers digest and interpret complex mechanisms and genomic datasets.


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.


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 webcite.

Pathway informatics; Genomic data analysis