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

@article{citeulike:1368861, 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 paper, 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.}, address = {Department of Bioinformatics, Bio-pharmaceutical Key Laboratory of Heilongjiang Province-Incubator of State Key Laboratory, Harbin Medical University, Harbin 150086, China.}, author = {Guo, Zheng and Li, Yongjin and Gong, Xue and Yao, Chen and Ma, Wencai and Wang, Dong and Li, Yanhui and Zhu, Jing and Zhang, Min and Yang, Da and Wang, Jing }, citeulike-article-id = {1368861}, doi = {http://dx.doi.org/10.1093/bioinformatics/btm294}, issn = {1460-2059}, journal = {Bioinformatics}, keywords = {interaction, network, protein}, month = {June}, posted-at = {2007-09-17 09:41:41}, priority = {2}, title = {Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network.}, url = {http://dx.doi.org/10.1093/bioinformatics/btm294}, year = {2007} }

TY - JOUR ID - citeulike:1368861 L3 - citeulike-article-id:1368861 TI - Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network. JF - Bioinformatics AD - Department of Bioinformatics, Bio-pharmaceutical Key Laboratory of Heilongjiang Province-Incubator of State Key Laboratory, Harbin Medical University, Harbin 150086, China. SN - 1460-2059 N2 - 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 paper, 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. KW - interaction KW - network KW - protein AU - Guo, Zheng AU - Li, Yongjin AU - Gong, Xue AU - Yao, Chen AU - Ma, Wencai AU - Wang, Dong AU - Li, Yanhui AU - Zhu, Jing AU - Zhang, Min AU - Yang, Da AU - Wang, Jing PY - 2007/06/01/ UR - http://dx.doi.org/10.1093/bioinformatics/btm294 ER -