title: An algorithm for finding functional modules and protein complexes in protein-protein interaction networks.
abstract: Biological processes are often performed by a group of proteins rather than by individual proteins, and proteins in a same biological group form a densely connected subgraph in a protein-protein interaction network. Therefore, finding a densely connected subgraph provides useful information to predict the function or protein complex of uncharacterized proteins in the highly connected subgraph. We have developed an efficient algorithm and program for finding cliques and near-cliques in a protein-protein interaction network. Analysis of the interaction network of yeast proteins using the algorithm demonstrates that 59% of the near-cliques identified by our algorithm have at least one function shared by all the proteins within a near-clique, and that 56% of the near-cliques show a good agreement with the experimentally determined protein complexes catalogued in MIPS.
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: Yu
authors.initials: Y
authors.lastname: Chen
authors.forename: De-Shuang
authors.initials: DS
authors.lastname: Huang
authors.forename: Kyungsook
authors.initials: K
authors.lastname: Han
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D008954:Models, Biological; D005810:Multigene Family / Q000502:physiology*; D025941:Protein Interaction Mapping / Q000379:methods*; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*
chemical_list: D020543:Proteome