Journal
GENES & GENETIC SYSTEMS
Volume 90, Issue 5, Pages 317-324Publisher
GENETICS SOC JAPAN
DOI: 10.1266/ggs.15-00032
Keywords
Gene Ontology; protein; protein complex; protein interaction network; semantic similarity
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Protein complexes are aggregates of protein molecules that play important roles in biological processes. Detecting protein complexes from protein-protein interaction (PPI) networks is one of the most challenging problems in computational biology, and many computational methods have been developed to solve this problem. Generally, these methods yield high false positive rates. In this article, a semantic similarity measure between proteins, based on Gene Ontology (GO) structure, is applied to weigh PPI networks. Consequently, one of the well-known methods, COACH, has been improved to be compatible with weighted PPI networks for protein complex detection. The new method, WCOACH, is compared to the COACH, ClusterOne, IPCA, CORE, OH-PIN, HC-PIN and MCODE methods on several PPI networks such as DIP, Krogan, Gavin 2002 and MIPS. WCOACH can be applied as a fast and high-performance algorithm to predict protein complexes in weighted PPI networks. All data and programs are freely available at http://bioinformatics.aut.ac.ir/wcoach.
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