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Bioinformatics Advance Access published online on October 25, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn555
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Modularity of cellular networks shows general center-periphery polarization

Alexander E. Vinogradov

Institute of Cytology, Russian Academy of Sciences, St.Petersburg 194064, Russia

*To whom correspondence should be addressed. Prof. Alexander E. Vinogradov, E-mail: aevin{at}mail.cytspb.rssi.ru


  Abstract

The modular biology is supposed to be a bridge from the molecular to the systems biology. Using a new approach, it is shown here that the protein interaction networks of yeast S.cerevisiae and bacteria E.coli consist of two large-scale modularity layers, central and peripheral, separated by a zone of depressed modularity. This finding based on the analysis of network topology is further supported by the discovery that there are many more Gene Ontology categories (terms) and KEGG biochemical pathways that are overrepresented in the central and peripheral layers than in the intermediate zone. The categories of the central layer are mostly related to nuclear information processing, regulation and cell cycle, whereas the peripheral layer is dealing with various metabolic and energetic processes, transport and cell communication. A similar center-periphery polarization of modularity is found in the protein domain networks (‘built-in interactome’) and in a powergrid (as a non-biological example). These data suggest a ‘polarized modularity’ model of cellular networks where the central layer seems to be regulatory and to use information storage of the nucleus, whereas the peripheral layer seems devoted to more specialized tasks and environmental interactions, with a complex ‘bus’ between the layers.

Associate Editor: Prof. Alfonso Valencia

Received on June 18, 2008; revised on October 22, 2008; accepted on October 23, 2008

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