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

Chunlin Wang12*, Chris Ding3, Qiaofeng Yang1 and Stephen R Holbrook1*

Author Affiliations

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

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

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

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Genome Biology 2007, 8:R271  doi:10.1186/gb-2007-8-12-r271

Published: 21 December 2007

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.