title: ModuleSearch: finding functional modules in a protein-protein interaction network.
abstract: Many biological processes are performed by a group of proteins rather than by individual proteins. Proteins involved in the same biological process often form a densely connected sub-graph in a protein-protein interaction network. Therefore, finding a dense sub-graph provides useful information to predict the function or protein complex of uncharacterised proteins in the sub-graph. We developed a heuristic algorithm that finds functional modules in a protein-protein interaction network and visualises the modules. The algorithm has been implemented in a platform-independent, standalone program called ModuleSearch. In an interaction network of yeast proteins, ModuleSearch found 366 overlapping modules. Of the modules, 71% have a function shared by more than half the proteins in the module and 58% have a function shared by all proteins in the module. Comparison of ModuleSearch with other programs shows that ModuleSearch finds more sub-graphs than most other programs, yet a higher proportion of the sub-graphs correspond to known functional modules. ModuleSearch and sample data are freely available to academics at http://bclab.inha.ac.kr/ModuleSearch.
authors.affiliation: School of Computer Science and Engineering, Inha University, Incheon, 402-751, South Korea.
authors.forename: Guangyu
authors.initials: G
authors.lastname: Cui
authors.forename: Rojan
authors.initials: R
authors.lastname: Shrestha
authors.forename: Kyungsook
authors.initials: K
authors.lastname: Han
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D025941:Protein Interaction Mapping / Q000706:statistics & numerical data; D060066:Protein Interaction Maps; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D012984:Software
chemical_list: D029701:Saccharomyces cerevisiae Proteins