Year: 2014
Type: article
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.
Source: BMC Genomics
Institutions: Memorial Sloan Kettering Cancer Center, Bilkent University
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,090
Awards: G2967234001, Pathway Commons: Research Resource for Biological Pathways, Genomic Approaches to Deciphering Memory Circuits, National Resource for Network Biology (NRNB), Kümelenmiş ya da hiyerarşik ilişkisel bilginin sorgulanması, yerleşimi ve görselleştirilmesi, G9000103217, Cancer Center Support Grant
OpenAlex ID: W2066081314