ArticlePloS one2017
Evolution of protein-protein interaction networks in yeast.
Article in PloS one, 2017. 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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Who cites it
13 citing papers in PubMed, 35 citations in OpenAlex.
- Co-option of transcription factors drives evolution of quantitative disease resistance against a necrotrophic pathogen.The Plant cell · 2025Article
- Key interaction networks: Identifying evolutionarily conserved non-covalent interaction networks across protein families.Protein science : a publication of the Protein Society · 2024Article
- Brief Communication: The Predictable Network Topology of Evolutionary Genomic Constraint.Molecular biology and evolution · 2024Article
- A computational approach to rapidly design peptides that detect SARS-CoV-2 surface protein S.NAR genomics and bioinformatics · 2022Article
- Defining hierarchical protein interaction networks from spectral analysis of bacterial proteomes.eLife · 2022Article
- ProMoCell and ProModb: Web services for analyzing interaction-based functionally localized protein modules in a cell.Journal of molecular modeling · 2022Article
- Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids.Plant biotechnology journal · 2021Article
- Comparative Analyses of Gene Co-expression Networks: Implementations and Applications in the Study of Evolution.Frontiers in genetics · 2021Review
- Protein Complexes Form a Basis for Complex Hybrid Incompatibility.Frontiers in genetics · 2021Review
- pyProGA-A PyMOL plugin for protein residue network analysis.PloS one · 2021Article
- Aligning functional network constraint to evolutionary outcomes.BMC evolutionary biology · 2020Article
- Genetic interaction networks mediate individual statin drug response inNPJ systems biology and applications · 2019Article
- Leveraging User-Friendly Network Approaches to Extract Knowledge From High-ThroughputFrontiers in genetics · 2019Review
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Interest in the evolution of protein-protein and genetic interaction networks has been rising in recent years, but the lack of large-scale high quality comparative datasets has acted as a barrier. Here, we carried out a comparative analysis of computationally predicted protein-protein interaction (PPI) networks from five closely related yeast species. We used the Protein-protein Interaction Prediction Engine (PIPE), which uses a database of known interactions to make sequence-based PPI predictions, to generate high quality predicted interactomes. Simulated proteomes and corresponding PPI networks were used to provide null expectations for the extent and nature of PPI network evolution. We found strong evidence for conservation of PPIs, with lower than expected levels of change in PPIs for about a quarter of the proteome. Furthermore, we found that changes in predicted PPI networks are poorly predicted by sequence divergence. Our analyses identified a number of functional classes experiencing fewer PPI changes than expected, suggestive of purifying selection on PPIs. Our results demonstrate the added benefit of considering predicted PPI networks when studying the evolution of closely related organisms.
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