Skip Navigation



Nucleic Acids Research Advance Access published online on May 22, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp414
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (644K) Freely available
Right arrow Screen PDF (454K) Freely available
Right arrow Supplementary Data
Right arrowOA All Versions of this Article:
37/12/e88    most recent
gkp414v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Yosef, N.
Right arrow Articles by Sharan, R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Yosef, N.
Right arrow Articles by Sharan, R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

A complex-centric view of protein network evolution

Nir Yosef1, Martin Kupiec2, Eytan Ruppin1,3 and Roded Sharan1,*

1The Blavatnik School of Computer Science, 2Department of Molecular Microbiology and Biotechnology and 3School of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel

*To whom correspondence should be addressed. Tel: +972-3-640-7139; Fax: +972-3-640-9357; Email: roded{at}tau.ac.il

Received November 10, 2008. Revised April 30, 2009. Accepted May 2, 2009.

The recent availability of protein–protein interaction networks for several species makes it possible to study protein complexes in an evolutionary context. In this article, we present a novel network-based framework for reconstructing the evolutionary history of protein complexes. Our analysis is based on generalizing evolutionary measures for single proteins to the level of whole subnetworks, comprehensively considering a broad set of computationally derived complexes and accounting for both sequence and interaction changes. Specifically, we compute sets of orthologous complexes across species, and use these to derive evolutionary rate and age measures for protein complexes. We observe significant correlations between the evolutionary properties of a complex and those of its member proteins, suggesting that protein complexes form early in evolution and evolve as coherent units. Additionally, our approach enables us to directly quantify the extent to which gene duplication has played a role in the evolution of complexes. We find that about one quarter of the sets of orthologous complexes have originated from evolutionary cores of homodimers that underwent duplication and divergence, testifying to the important role of gene duplication in protein complex evolution.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.