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Bioinformatics Advance Access published online on May 15, 2009
Bioinformatics, 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,*

1Department of Computer Science, University of Texas at Dallas
2 Department of Molecular Biology, University of Texas at Dallas

*To whom correspondence should be addressed. Prof. Ying Liu, E-mail: ying.liu{at}utdallas.edu


  Abstract

Motivation: 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 networks at the meso-scale may provide insights into the presence and form of relationships between individual protein complexes and functional modules.

Results: Results: In this paper we present an efficient algorithm for performing subgraph 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 protein-protein interaction network of Saccharomyces cerevisiae.

Contact: ying.liu{at}utdallas.edu

Associate Editor: Dr. Trey Ideker

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

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