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