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 http://code.google.com/p/chibe.
authors.affiliation: Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, Box 460, New York, NY 10065, USA. chibe@cbio.mskcc.org.
authors.forename: Özgün
authors.initials: Ö
authors.lastname: Babur
authors.forename: Ugur
authors.initials: U
authors.lastname: Dogrusoz
authors.forename: Merve
authors.initials: M
authors.lastname: Çakır
authors.forename: Bülent Arman
authors.initials: BA
authors.lastname: Aksoy
authors.forename: Nikolaus
authors.initials: N
authors.lastname: Schultz
authors.forename: Chris
authors.initials: C
authors.lastname: Sander
authors.forename: Emek
authors.initials: E
authors.lastname: Demir
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D003196:Computer Graphics; D057225:Data Mining; D016889:Endometrial Neoplasms / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D005260:Female; D023281:Genomics / Q000379:methods*; D006801:Humans; D012984:Software
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