ArticleBMC bioinformatics2009
Phylogeny-guided interaction mapping in seven eukaryotes.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 17 citations in OpenAlex.
- Computational identification of protein-protein interactions in model plant proteomes.Scientific reports · 2019Article
- In silico prediction of protein-protein interactions in human macrophages.BMC research notes · 2014Article
- A probabilistic model of neutral and selective dynamics of protein network evolution.Journal of computational biology : a journal of computational molecular cell biology · 2013Article
- CoPAP: Coevolution of presence-absence patterns.Nucleic acids research · 2013Article
- Uncovering the co-evolutionary network among prokaryotic genes.Bioinformatics (Oxford, England) · 2012Article
- Evolution of gene neighborhoods within reconciled phylogenies.Bioinformatics (Oxford, England) · 2012Article
- Article
- What evidence is there for the homology of protein-protein interactions?PLoS computational biology · 2012Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe assembly of reliable and complete protein-protein interaction (PPI) maps remains one of the significant challenges in systems biology. Computational methods which integrate and prioritize interaction data can greatly aid in approaching this goal.
resultsWe developed a Bayesian inference framework which uses phylogenetic relationships to guide the integration of PPI evidence across multiple datasets and species, providing more accurate predictions. We apply our framework to reconcile seven eukaryotic interactomes: H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. cerevisiae and A. thaliana. Comprehensive GO-based quality assessment indicates a 5% to 44% score increase in predicted interactomes compared to the input data. Further support is provided by gold-standard MIPS, CYC2008 and HPRD datasets. We demonstrate the ability to recover known PPIs in well-characterized yeast and human complexes (26S proteasome, endosome and exosome) and suggest possible new partners interacting with the putative SWI/SNF chromatin remodeling complex in A. thaliana.
conclusionOur phylogeny-guided approach compares favorably to two standard methods for mapping PPIs across species. Detailed analysis of predictions in selected functional modules uncovers specific PPI profiles among homologous proteins, establishing interaction-based partitioning of protein families. Provided evidence also suggests that interactions within core complex subunits are in general more conserved and easier to transfer accurately to other organisms, than interactions between these subunits.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.