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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

Abstract

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 http://code.google.com/p/chibe webcite.

Keywords:
Pathway informatics; Genomic data analysis