Integrating biological pathways and genomic profiles with ChiBE 2

Ozgun Babur, Ugur Dogrusoz, Merve C¸akir, Bu¨lent A. Aksoy, Nikolaus Schultz, Chris Sander, Emek Demir

Research output: Contribution to journalArticle

12 Citations (Scopus)

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.

Original languageEnglish (US)
Article number642
JournalBMC Genomics
Volume15
Issue number1
DOIs
StatePublished - Aug 3 2014
Externally publishedYes

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Genomics
Software
Research Personnel
Workflow
Databases
Gene Expression
Neoplasms

Keywords

  • Genomic data analysis
  • Pathway informatics

ASJC Scopus subject areas

  • Biotechnology
  • Genetics
  • Medicine(all)

Cite this

Babur, O., Dogrusoz, U., C¸akir, M., Aksoy, B. A., Schultz, N., Sander, C., & Demir, E. (2014). Integrating biological pathways and genomic profiles with ChiBE 2. BMC Genomics, 15(1), [642]. https://doi.org/10.1186/1471-2164-15-642

Integrating biological pathways and genomic profiles with ChiBE 2. / Babur, Ozgun; Dogrusoz, Ugur; C¸akir, Merve; Aksoy, Bu¨lent A.; Schultz, Nikolaus; Sander, Chris; Demir, Emek.

In: BMC Genomics, Vol. 15, No. 1, 642, 03.08.2014.

Research output: Contribution to journalArticle

Babur, O, Dogrusoz, U, C¸akir, M, Aksoy, BA, Schultz, N, Sander, C & Demir, E 2014, 'Integrating biological pathways and genomic profiles with ChiBE 2', BMC Genomics, vol. 15, no. 1, 642. https://doi.org/10.1186/1471-2164-15-642
Babur O, Dogrusoz U, C¸akir M, Aksoy BA, Schultz N, Sander C et al. Integrating biological pathways and genomic profiles with ChiBE 2. BMC Genomics. 2014 Aug 3;15(1). 642. https://doi.org/10.1186/1471-2164-15-642
Babur, Ozgun ; Dogrusoz, Ugur ; C¸akir, Merve ; Aksoy, Bu¨lent A. ; Schultz, Nikolaus ; Sander, Chris ; Demir, Emek. / Integrating biological pathways and genomic profiles with ChiBE 2. In: BMC Genomics. 2014 ; Vol. 15, No. 1.
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