title: Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Bioinformatics, Bio-pharmaceutical Key Laboratory of Heilongjiang Province-Incubator of State Key Laboratory, Harbin Medical University, Harbin 150086, China. guoz@ems.hrbmu.edu.cn
authors.forename: Zheng
authors.initials: Z
authors.lastname: Guo
authors.forename: Lei
authors.initials: L
authors.lastname: Wang
authors.forename: Yongjin
authors.initials: Y
authors.lastname: Li
authors.forename: Xue
authors.initials: X
authors.lastname: Gong
authors.forename: Chen
authors.initials: C
authors.lastname: Yao
authors.forename: Wencai
authors.initials: W
authors.lastname: Ma
authors.forename: Dong
authors.initials: D
authors.lastname: Wang
authors.forename: Yanhui
authors.initials: Y
authors.lastname: Li
authors.forename: Jing
authors.initials: J
authors.lastname: Zhu
authors.forename: Min
authors.initials: M
authors.lastname: Zhang
authors.forename: Da
authors.initials: D
authors.lastname: Yang
authors.forename: Shaoqi
authors.initials: S
authors.lastname: Rao
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D008954:Models, Biological; D025941:Protein Interaction Mapping / Q000379:methods*; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*
chemical_list: D020543:Proteome