Integrating biological pathways and genomic profiles with ChiBE 2
Aksoy, B. A.
BioMed Central Ltd.
Babur, Ö., Dogrusoz, U., Çakır, M., Aksoy, B. A., Schultz, N., Sander, C., & Demir, E. (2014). Integrating biological pathways and genomic profiles with ChiBE 2. BMC genomics, 15(1), 1.
Please cite this item using this persistent URLhttp://hdl.handle.net/11693/12684
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.