ArticleNucleic acids research2009
A complex-centric view of protein network evolution.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 29 citations in OpenAlex.
- ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies.Genome research · 2025Article
- ERC 2.0 - evolutionary rate covariation update improves inference of functional interactions across large phylogenies.bioRxiv : the preprint server for biology · 2025Article
- Do long telomeres affect cellular fitness?Current genetics · 2018Review
- Conservation of Nonsense-Mediated mRNA Decay Complex Components Throughout Eukaryotic Evolution.Scientific reports · 2017Article
- ANAT 2.0: reconstructing functional protein subnetworks.BMC bioinformatics · 2017Article
- Systematic identification and correction of annotation errors in the genetic interaction map of Saccharomyces cerevisiae.Nucleic acids research · 2016Article
- In Silico Designing and Analysis of Inhibitors against Target Protein Identified through Host-Pathogen Protein Interactions in Malaria.International journal of medicinal chemistry · 2016Article
- Detecting conserved protein complexes using a dividing-and-matching algorithm and unequally lenient criteria for network comparison.Algorithms for molecular biology : AMB · 2015Article
- SH3 interactome conserves general function over specific form.Molecular systems biology · 2013Article
- A methodology for detecting the orthology signal in a PPI network at a functional complex level.BMC bioinformatics · 2012Article
- Comparative interaction networks: bridging genotype to phenotype.Advances in experimental medicine and biology · 2012Review
- Lateral acquisition of genes is affected by the friendliness of their products.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- The Modular Organization of Protein Interactions in Escherichia coli.PLoS computational biology · 2009Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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