ArticlePLoS computational biology2008
Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence.
Article in PLoS computational biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Comparative analysis of m6A mRNA modification inFrontiers in genetics · 2026Article
- The genetic factors of bilaterian evolution.eLife · 2020Article
- NAPAbench 2: A network synthesis algorithm for generating realistic protein-protein interaction (PPI) network families.PloS one · 2020Article
- A review of protein-protein interaction network alignment: From pathway comparison to global alignment.Computational and structural biotechnology journal · 2020Review
- The Evolutionary Traceability of a Protein.Genome biology and evolution · 2019Article
- Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant.Nucleic acids research · 2018Article
- Protein-protein binding selectivity and network topology constrain global and local properties of interface binding networks.Scientific reports · 2017Article
- Nonlinear growth: an origin of hub organization in complex networks.Royal Society open science · 2017Article
- A genome wide dosage suppressor network reveals genomic robustness.Nucleic acids research · 2017Article
- Towards Consensus Gene Ages.Genome biology and evolution · 2016Article
- Evolution of intraspecific transcriptomic landscapes in yeasts.Nucleic acids research · 2015Article
- Gene age predicts the strength of purifying selection acting on gene expression variation in humans.American journal of human genetics · 2014Article
- Dissecting the human protein-protein interaction network via phylogenetic decomposition.Scientific reports · 2014Article
- GASOLINE: a Greedy And Stochastic algorithm for optimal Local multiple alignment of Interaction NEtworks.PloS one · 2014Article
- How old is my gene?Trends in genetics : TIG · 2013Review
- Extensive rewiring and complex evolutionary dynamics in a C. elegans multiparameter transcription factor network.Molecular cell · 2013Article
- Proteome-wide prediction of self-interacting proteins based on multiple properties.Molecular & cellular proteomics : MCP · 2013Article
- A kinetic model of the evolution of a protein interaction network.BMC genomics · 2013Article
- SMETANA: accurate and scalable algorithm for probabilistic alignment of large-scale biological networks.PloS one · 2013Article
- Preferential duplication of intermodular hub genes: an evolutionary signature in eukaryotes genome networks.PloS one · 2013Article
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2 authors.
Funding
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.
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