Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence Export

@article{kim_08_agedependent, abstract = {Proteins interact in complex protein–protein interaction (PPI) networks whose topological properties—such as scale-free topology, hierarchical modularity, and dissortativity—have suggested models of network evolution. Currently preferred models invoke preferential attachment or gene duplication and divergence to produce networks whose topology matches that observed for real PPIs, thus supporting these as likely models for network evolution. Here, we show that the interaction density and homodimeric frequency are highly protein age–dependent in real PPI networks in a manner which does not agree with these canonical models. In light of these results, we propose an alternative stochastic model, which adds each protein sequentially to a growing network in a manner analogous to protein crystal growth (CG) in solution. The key ideas are (1) interaction probability increases with availability of unoccupied interaction surface, thus following an anti-preferential attachment rule, (2) as a network grows, highly connected sub-networks emerge into protein modules or complexes, and (3) once a new protein is committed to a module, further connections tend to be localized within that module. The CG model produces PPI networks consistent in both topology and age distributions with real PPI networks and is well supported by the spatial arrangement of protein complexes of known 3-D structure, suggesting a plausible physical mechanism for network evolution.}, author = {Kim, Wan K. and Marcotte, Edward M.}, citeulike-article-id = {3727486}, citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.1000232}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19043579}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19043579}, comment = {Similar conclusions as villar\_08\_selfassembly http://www.citeulike.org/user/chad\_davis/article/3807048 }, day = {28}, doi = {10.1371/journal.pcbi.1000232}, journal = {PLoS Comput Biol}, keywords = {complexes, evolution, networks, ppi, proj\_assembly, proj\_interprets, statistics, validation}, month = {November}, number = {11}, pages = {e1000232+}, posted-at = {2008-12-19 09:35:41}, priority = {3}, publisher = {Public Library of Science}, title = {Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence}, url = {http://dx.doi.org/10.1371/journal.pcbi.1000232}, volume = {4}, year = {2008} }

TY - JOUR ID - kim_08_agedependent L3 - citeulike-article-id:3727486 N2 - Proteins interact in complex protein–protein interaction (PPI) networks whose topological properties—such as scale-free topology, hierarchical modularity, and dissortativity—have suggested models of network evolution. Currently preferred models invoke preferential attachment or gene duplication and divergence to produce networks whose topology matches that observed for real PPIs, thus supporting these as likely models for network evolution. Here, we show that the interaction density and homodimeric frequency are highly protein age–dependent in real PPI networks in a manner which does not agree with these canonical models. In light of these results, we propose an alternative stochastic model, which adds each protein sequentially to a growing network in a manner analogous to protein crystal growth (CG) in solution. The key ideas are (1) interaction probability increases with availability of unoccupied interaction surface, thus following an anti-preferential attachment rule, (2) as a network grows, highly connected sub-networks emerge into protein modules or complexes, and (3) once a new protein is committed to a module, further connections tend to be localized within that module. The CG model produces PPI networks consistent in both topology and age distributions with real PPI networks and is well supported by the spatial arrangement of protein complexes of known 3-D structure, suggesting a plausible physical mechanism for network evolution. IS - 11 JF - PLoS Comput Biol TI - Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence PB - Public Library of Science VL - 4 SP - e1000232 KW - complexes KW - evolution KW - networks KW - ppi KW - proj_assembly KW - proj_interprets KW - statistics KW - validation N1 - Similar conclusions as villar_08_selfassembly http://www.citeulike.org/user/chad_davis/article/3807048 AU - Kim, Wan AU - Marcotte, Edward PY - 2008/11/28/ UR - http://dx.doi.org/10.1371/journal.pcbi.1000232 ER -