ArticlePLoS computational biology2012
What evidence is there for the homology of protein-protein interactions?
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Structure-function relationship of the Pseudomonas aeruginosa AsmA-like proteins YhdP and YdbH involved in outer membrane biogenesis.Protein science : a publication of the Protein Society · 2025Article
- Enhancing coevolutionary signals in protein-protein interaction prediction through clade-wise alignment integration.Scientific reports · 2024Article
- Classification in biological networks with hypergraphlet kernels.Bioinformatics (Oxford, England) · 2021Article
- Xeroderma pigmentosum A homolog fromJournal of biosciences · 2021Article
- Integration of Heterogeneous Experimental Data Improves Global Map of Human Protein Complexes.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2019Article
- Cross-kingdom auxiliary subunit modulation of a voltage-gated sodium channel.The Journal of biological chemistry · 2018Article
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- Cell cycle progression in Caulobacter requires a nucleoid-associated protein with high AT sequence recognition.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
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- Sequence specificity between interacting and non-interacting homologs identifies interface residues--a homodimer and monomer use case.BMC bioinformatics · 2015Article
- Structural Perspectives on the Evolutionary Expansion of Unique Protein-Protein Binding Sites.Biophysical journal · 2015Article
- Modularity and predictability in cell signaling and decision making.Molecular biology of the cell · 2014Article
- Alignment-free protein interaction network comparison.Bioinformatics (Oxford, England) · 2014Article
- Using biological networks to improve our understanding of infectious diseases.Computational and structural biotechnology journal · 2014Review
- Protein flexibility facilitates quaternary structure assembly and evolution.PLoS biology · 2014Article
- Synthetic genetic array screen identifies PP2A as a therapeutic target in Mad2-overexpressing tumors.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Loss of optineurin in vivo results in elevated cell death and alters axonal trafficking dynamics.PloS one · 2014Article
- Article
- Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review.Pharmacology & therapeutics · 2013Review
- Complementing the Eukaryotic Protein Interactome.PloS one · 2013Article
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Authors and funding
4 authors.
Funding
Abstract
The notion that sequence homology implies functional similarity underlies much of computational biology. In the case of protein-protein interactions, an interaction can be inferred between two proteins on the basis that sequence-similar proteins have been observed to interact. The use of transferred interactions is common, but the legitimacy of such inferred interactions is not clear. Here we investigate transferred interactions and whether data incompleteness explains the lack of evidence found for them. Using definitions of homology associated with functional annotation transfer, we estimate that conservation rates of interactions are low even after taking interactome incompleteness into account. For example, at a blastp E-value threshold of 10(-70), we estimate the conservation rate to be about 11 % between S. cerevisiae and H. sapiens. Our method also produces estimates of interactome sizes (which are similar to those previously proposed). Using our estimates of interaction conservation we estimate the rate at which protein-protein interactions are lost across species. To our knowledge, this is the first such study based on large-scale data. Previous work has suggested that interactions transferred within species are more reliable than interactions transferred across species. By controlling for factors that are specific to within-species interaction prediction, we propose that the transfer of interactions within species might be less reliable than transfers between species. Protein-protein interactions appear to be very rarely conserved unless very high sequence similarity is observed. Consequently, inferred interactions should be used with care.
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