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Nucleic Acids Research 2006 34(9):2812-2819; doi:10.1093/nar/gkl325
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Published online 22 May 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

Yeast Protein Interactome topology provides framework for coordinated-functionality

André X. C. N. Valente* and Michael E. Cusick1,2

Biometry Research Group, Department of Health and Human Services, National Cancer Institute, National Institutes of Health Bethesda, MD 20892, USA 1 Center for Cancer Systems Biology and Deptartment of Cancer Biology, Dana-Farber Cancer Institute Boston, MA 02115, USA 2 Deptartment of Genetics, Harvard Medical School Boston, MA 02115, USA

*To whom correspondence should be addressed. Tel: +1 301 496 8550; Fax: +1 301 402 0816; Email: andre{at}deas.harvard.edu

Received January 12, 2006. Revised February 20, 2006. Accepted April 13, 2006.

The architecture of the network of protein–protein physical interactions in Saccharomyces cerevisiae is exposed through the combination of two complementary theoretical network measures, betweenness centrality and ‘Q-modularity’. The yeast interactome is characterized by well-defined topological modules connected via a small number of inter-module protein interactions. Should such topological inter-module connections turn out to constitute a form of functional coordination between the modules, we speculate that this coordination is occurring typically in a pairwise fashion, rather than by way of high-degree hub proteins responsible for coordinating multiple modules. The unique non-hub-centric hierarchical organization of the interactome is not reproduced by gene duplication-and-divergence stochastic growth models that disregard global selective pressures.


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