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Bioinformatics Advance Access originally published online on May 15, 2009
Bioinformatics 2009 25(14):1814-1821; doi:10.1093/bioinformatics/btp297
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Structure discovery in PPI networks using pattern-based network decomposition

Philip Bachman 1 and Ying Liu 1,2,*

1 Department of Computer Science and 2 Department of Molecular Biology, University of Texas at Dallas, Richardson, TX 75083-0688

* To whom correspondence should be addressed.


  Abstract

Motivation: The large, complex networks of interactions between proteins provide a lens through which one can examine the structure and function of biological systems. Previous analyses of these continually growing networks have primarily followed either of two approaches: large-scale statistical analysis of holistic network properties, or small-scale analysis of local topological features. Meanwhile, investigation of meso-scale network structure (above that of individual functional modules, while maintaining the significance of individual proteins) has been hindered by the computational complexity of structural search in networks. Examining protein–protein interaction (PPI) networks at the meso-scale may provide insights into the presence and form of relationships between individual protein complexes and functional modules.

Results: In this article, we present an efficient algorithm for performing sub-graph isomorphism queries on a network and show its computational advantage over previous methods. We also present a novel application of this form of topological search which permits analysis of a network's structure at a scale between that of individual functional modules and that of network-wide properties. This analysis provides support for the presence of hierarchical modularity in the PPI network of Saccharomyces cerevisiae.

Contact: ying.liu{at}utdallas.edu

Associate Editor: Trey Ideker

Received on December 1, 2008; revised on March 16, 2009; accepted on April 28, 2009

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