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Bioinformatics. 2007 Aug 15;23(16):2121-8. Epub 2007 Jun 1.

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

Author information

Department of Bioinformatics, Bio-pharmaceutical Key Laboratory of Heilongjiang Province-Incubator of State Key Laboratory, Harbin Medical University, Harbin 150086, China.

Erratum in

  • Bioinformatics. 2009 Jun 15;25(12):1574. Wang, Lei [added]; Rao, Shaoqi [added].



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.


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.


Supplementary data are available at Bioinformatics online.

[Indexed for MEDLINE]

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