Integrating biological pathways and genomic profiles with ChiBE 2
dc.citation.epage | 9 | en_US |
dc.citation.issueNumber | 642 | en_US |
dc.citation.spage | 1 | en_US |
dc.citation.volumeNumber | 15 | en_US |
dc.contributor.author | Babur, O. | en_US |
dc.contributor.author | Dogrusoz, U. | en_US |
dc.contributor.author | Çakır, M. | en_US |
dc.contributor.author | Aksoy, B. A. | en_US |
dc.contributor.author | Schultz, N. | en_US |
dc.contributor.author | Sander, C. | en_US |
dc.contributor.author | Demir, E. | en_US |
dc.date.accessioned | 2016-02-08T10:46:48Z | |
dc.date.available | 2016-02-08T10:46:48Z | |
dc.date.issued | 2014 | en_US |
dc.department | Department of Computer Engineering | en_US |
dc.description.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. © 2014 Babur et al.; licensee BioMed Central Ltd. | en_US |
dc.description.provenance | Made available in DSpace on 2016-02-08T10:46:48Z (GMT). No. of bitstreams: 1 bilkent-research-paper.pdf: 70227 bytes, checksum: 26e812c6f5156f83f0e77b261a471b5a (MD5) Previous issue date: 2014 | en |
dc.identifier.doi | 10.1186/1471-2164-15-642 | en_US |
dc.identifier.issn | 1471-2164 | |
dc.identifier.uri | http://hdl.handle.net/11693/25558 | |
dc.language.iso | English | en_US |
dc.publisher | BioMed Central Ltd. | en_US |
dc.relation.isversionof | http://dx.doi.org/10.1186/1471-2164-15-642 | en_US |
dc.source.title | BMC Genomics | en_US |
dc.subject | Genomic data analysis | en_US |
dc.subject | Pathway informatics | en_US |
dc.subject | Automation | en_US |
dc.subject | Biology | en_US |
dc.subject | Computer graphics | en_US |
dc.subject | Computer program | en_US |
dc.subject | Gene expression | en_US |
dc.subject | Genomics | en_US |
dc.subject | Information processing | en_US |
dc.subject | Intermethod comparison | en_US |
dc.subject | Molecular genetics | en_US |
dc.subject | Breast tumor | en_US |
dc.subject | Endometrial neoplasms | en_US |
dc.subject | Software | en_US |
dc.title | Integrating biological pathways and genomic profiles with ChiBE 2 | en_US |
dc.type | Article | en_US |
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