Integrating biological pathways and genomic profiles with ChiBE 2

被引:19
作者
Babur, Oezguen [1 ]
Dogrusoz, Ugur [2 ]
Cakir, Merve [2 ]
Aksoy, Buelent Arman [1 ,3 ]
Schultz, Nikolaus [1 ]
Sander, Chris [1 ]
Demir, Emek [1 ]
机构
[1] Mem Sloan Kettering Canc Ctr, Computat Biol Ctr, New York, NY 10065 USA
[2] Bilkent Univ, Dept Comp Engn, TR-06800 Ankara, Turkey
[3] Triinst Training Program Computat Biol & Med, New York, NY 10065 USA
来源
BMC GENOMICS | 2014年 / 15卷
基金
美国国家卫生研究院;
关键词
Pathway informatics; Genomic data analysis; MODULES;
D O I
10.1186/1471-2164-15-642
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
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.
引用
收藏
页数:9
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