Journal of Biomedicine and Biotechnology 
Volume 2008 (2008), Article ID 860270, 10 pages
doi:10.1155/2008/860270
Research Article

An Algorithm for Finding Functional Modules and Protein Complexes in Protein-Protein Interaction Networks

Guangyu Cui,1 Yu Chen,1 De-Shuang Huang,2 and Kyungsook Han1

 1School of Computer Science and Engineering, Inha University, Incheon 402-751, South Korea
2Hefei Institute of Intelligent Machines, Chinese Academy of Sciences, China
Received 1 September 2007; Revised 12 November 2007; Accepted 24 December 2007

Recommended by Daniel Howard

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.