title: Identifying protein complexes and functional modules--from static PPI networks to dynamic PPI networks.
abstract: Cellular processes are typically carried out by protein complexes and functional modules. Identifying them plays an important role for our attempt to reveal principles of cellular organizations and functions. In this article, we review computational algorithms for identifying protein complexes and/or functional modules from protein-protein interaction (PPI) networks. We first describe issues and pitfalls when interpreting PPI networks. Then based on types of data used and main ideas involved, we briefly describe protein complex and/or functional module identification algorithms in four categories: (i) those based on topological structures of unweighted PPI networks; (ii) those based on characters of weighted PPI networks; (iii) those based on multiple data integrations; and (iv) those based on dynamic PPI networks. The PPI networks are modelled increasingly precise when integrating more types of data, and the study of protein complexes would benefit by shifting from static to dynamic PPI networks.
authors.affiliation: School of Computer, Wuhan University, Wuhan 430072, China. Tel.: +86-27-6877-5711; Fax: +86-27-6877-5711; liujuan@whu.edu.cn; Fang-Xiang Wu, College of Engineering, University of Saskatchewan, 57 Campus Drive, Saskatoon, SK S7N 5A9, Canada. Tel.: +1-306-966-5280; Fax: +1-306-966-5427; E-mail: faw341@mail.usask.ca.
authors.forename: Bolin
authors.initials: B
authors.lastname: Chen
authors.forename: Weiwei
authors.initials: W
authors.lastname: Fan
authors.forename: Juan
authors.initials: J
authors.lastname: Liu
authors.forename: Fang-Xiang
authors.initials: FX
authors.lastname: Wu
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D025941:Protein Interaction Mapping / Q000706:statistics & numerical data*; D060066:Protein Interaction Maps
chemical_list: D046912:Multiprotein Complexes
keywords: dynamic network; functional module; protein complex; protein–protein interaction; static network