Method

Consistent dissection of the protein interaction network by combining global and local metrics

Chunlin Wang^1,2 , Chris Ding³ , Qiaofeng Yang¹ and Stephen R Holbrook¹

¹Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA

²Division of Infectious Diseases, School of Medicine, Stanford University, Stanford, CA 94035, USA

³Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA

author email corresponding author email

Genome Biology 2007, 8:R271doi:10.1186/gb-2007-8-12-r271

Published:	21 December 2007

Subject areas: Bioinformatics, Genome studies

Abstract

We propose a new network decomposition method to systematically identify protein interaction modules in the protein interaction network. Our method incorporates both a global metric and a local metric for balance and consistency. We have compared the performance of our method with several earlier approaches on both simulated and real datasets using different criteria, and show that our method is more robust to network alterations and more effective at discovering functional protein modules.