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Bioinformatics Advance Access published online on February 17, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp083
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Homogeneous decomposition of protein interaction networks: refining the description of intra-modular interactions

Géraldine Del Mondo 1, Damien Eveillard 1 and Irena Rusu 1,*

1Computational Biology group (ComBi) - LINA, Université de Nantes, CNRS UMR 6241, 2 rue de la Houssini`ere, 44300 Nantes, France

*To whom correspondence should be addressed. Irena Rusu, E-mail: irena.rusu{at}univ-nantes.fr


  Abstract

Motivation: Modules in biology appeared quickly as an accurate way for summarizing complex living systems by simple ones. Therefore, finding an appropriate relationship between modules extracted from a biological graph and proteic complexes remains a crucial task. Recent studies successfully proposed various descriptions of protein interaction networks. These approaches succeed in showing modules within the network and how the modules interact. However, describing the interactions within the modules, i.e. intra-modular interactions, remains little analyzed despite its interest for understanding module functions.

Results: We overcome this weakness by adding a complementary description to the already successful approaches: a hierarchical decomposition named homogeneous decomposition. This decomposition represents a natural refinement of previous analyses and details interactions within a module. We propose to illustrate these improvements by three practical cases. Among them, we decompose the yeast protein interaction network and show reachable biological insights that might be extracted from a complex large-scale network.

Availability: A program is at disposal under CeCILL license at: www.lina.univ-nantes.fr/combi/DH/Home.html

Contact: irena.rusu{at}univ-nantes.fr

Associate Editor: Prof. Burkhard Rost

Received on March 28, 2008; revised on February 10, 2009; accepted on February 10, 2009

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