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Bioinformatics Advance Access originally published online on June 1, 2007
Bioinformatics 2007 23(16):2121-2128; doi:10.1093/bioinformatics/btm294
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Edge-based scoring and searching method for identifying condition-responsive protein–protein interaction sub-network

Zheng Guo 1,2,*,{dagger}, Yongjin Li 1,{dagger}, Xue Gong 1, Chen Yao 1, Wencai Ma 1, Dong Wang 1, Yanhui Li 1, Jing Zhu 1, Min Zhang 1, Da Yang 1 and Jing Wang 1

1Department of Bioinformatics, Bio-pharmaceutical Key Laboratory of Heilongjiang Province-Incubator of State Key Laboratory, Harbin Medical University, Harbin 150086 and 2Bioinformatics Centre and School of Life Science, University of Electronic Science and Technology of China, Chengdu, 610054, China

*To whom correspondence should be addressed.


  Abstract

Motivation: Current high-throughput protein–protein interaction (PPI) data do not provide information about the condition(s) under which the interactions occur. Thus, the identification of condition-responsive PPI sub-networks is of great importance for investigating how a living cell adapts to changing environments.

Results: In this article, we propose a novel edge-based scoring and searching approach to extract a PPI sub-network responsive to conditions related to some investigated gene expression profiles. Using this approach, what we constructed is a sub-network connected by the selected edges (interactions), instead of only a set of vertices (proteins) as in previous works. Furthermore, we suggest a systematic approach to evaluate the biological relevance of the identified responsive sub-network by its ability of capturing condition-relevant functional modules. We apply the proposed method to analyze a human prostate cancer dataset and a yeast cell cycle dataset. The results demonstrate that the edge-based method is able to efficiently capture relevant protein interaction behaviors under the investigated conditions.

Contact: guoz{at}ems.hrbmu.edu.cn

Supplementary information: Supplementary data are available at Bioinformatics online.

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be declared as joint First Authors.

Received on January 14, 2007; revised on May 19, 2007; accepted on May 25, 2007

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