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Bioinformatics. 2008 Jun 15;24(12):1442-7. doi: 10.1093/bioinformatics/btn200. Epub 2008 Apr 23.

A global pathway crosstalk network.

Author information

  • 1Computational Biology, GlaxoSmithKline R&D, 709 Swedeland Road, UMW2230, King of Prussia, PA 19406, USA. yong.2.li@gsk.com

Abstract

MOTIVATION:

Given the complex nature of biological systems, pathways often need to function in a coordinated fashion in order to produce appropriate physiological responses to both internal and external stimuli. Therefore, understanding the interaction and crosstalk between pathways is important for understanding the function of both cells and more complex systems.

RESULTS:

We have developed a computational approach to detect crosstalk among pathways based on protein interactions between the pathway components. We built a global mammalian pathway crosstalk network that includes 580 pathways (covering 4753 genes) with 1815 edges between pathways. This crosstalk network follows a power-law distribution: P(k) approximately k(-)(gamma), gamma = 1.45, where P(k) is the number of pathways with k neighbors, thus pathway interactions may exhibit the same scale-free phenomenon that has been documented for protein interaction networks. We further used this network to understand colorectal cancer progression to metastasis based on transcriptomic data.

CONTACT:

yong.2.li@gsk.com

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
18434343
[PubMed - indexed for MEDLINE]
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