Integrating biological pathways and genomic profiles with ChiBE 2 Journal Article

Authors: Babur, O.; Dogrusoz, U.; Çakır, M.; Aksoy, B. A.; Schultz, N.; Sander, C.; Demir, E.
Article Title: Integrating biological pathways and genomic profiles with ChiBE 2
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
Keywords: molecular genetics; gene expression; biology; data base; automation; information processing; genomics; intermethod comparison; computer program; computer graphics; article; genomic data analysis; pathway informatics
Journal Title: BMC Genomics
Volume: 15
ISSN: 1471-2164
Publisher: Biomed Central Ltd  
Date Published: 2014-08-03
Start Page: 642
Language: English
DOI: 10.1186/1471-2164-15-642
PROVIDER: scopus
PMCID: PMC4131037
PUBMED: 25086704
Notes: Export Date: 2 September 2014 -- CODEN: BGMEE -- Source: Scopus
Citation Impact
MSK Authors
  1. Ozgun Babur
    12 Babur
  2. Chris Sander
    204 Sander
  3. Emek Demir
    27 Demir
  4. Nikolaus D Schultz
    283 Schultz
  5. Bulent Arman Aksoy
    35 Aksoy