ArticleBioinformatics (Oxford, England)2012
Uncovering the co-evolutionary network among prokaryotic genes.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Genome-based assessment of antimicrobial resistance reveals the lineage specificity of resistance and resistance gene profiles inMicrobiology spectrum · 2024Article
- Coevolution of the CDCA7-HELLS ICF-related nucleosome remodeling complex and DNA methyltransferases.eLife · 2023Article
- Coevolution of the CDCA7-HELLS ICF-related nucleosome remodeling complex and DNA methyltransferases.bioRxiv : the preprint server for biology · 2023Article
- The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles.Systematic biology · 2023Article
- Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes.BMC bioinformatics · 2023Article
- Inverse Potts model improves accuracy of phylogenetic profiling.Bioinformatics (Oxford, England) · 2022Article
- Robustness of Phylogenetic Inference to Model Misspecification Caused by Pairwise Epistasis.Molecular biology and evolution · 2021Article
- Evidence for Selection in the Abundant Accessory Gene Content of a Prokaryote Pangenome.Molecular biology and evolution · 2021Article
- Public good exploitation in natural bacterioplankton communities.Science advances · 2021Article
- Horizontal Gene Transfer as a Source of Conflict and Cooperation in Prokaryotes.Frontiers in microbiology · 2020Article
- A multi-scale coevolutionary approach to predict interactions between protein domains.PLoS computational biology · 2019Article
- Phylogenetic Clustering of Genes Reveals Shared Evolutionary Trajectories and Putative Gene Functions.Genome biology and evolution · 2018Article
- A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination.PLoS computational biology · 2018Article
- Evolutionary assembly patterns of prokaryotic genomes.Genome research · 2016Article
- Diversification and coevolution of the ghrelin/growth hormone secretagogue receptor system in vertebrates.Ecology and evolution · 2016Article
- Efficient Gene Tree Correction Guided by Genome Evolution.PloS one · 2016Article
- Evolution of chemical diversity by coordinated gene swaps in type II polyketide gene clusters.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Practical aspects of protein co-evolution.Frontiers in cell and developmental biology · 2014Review
- Reconciliation-based detection of co-evolving gene families.BMC bioinformatics · 2013Article
- CoPAP: Coevolution of presence-absence patterns.Nucleic acids research · 2013Article
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Authors and funding
4 authors.
Funding
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Abstract
motivationCorrelated events of gains and losses enable inference of co-evolution relations. The reconstruction of the co-evolutionary interactions network in prokaryotic species may elucidate functional associations among genes.
resultsWe developed a novel probabilistic methodology for the detection of co-evolutionary interactions between pairs of genes. Using this method we inferred the co-evolutionary network among 4593 Clusters of Orthologous Genes (COGs). The number of co-evolutionary interactions substantially differed among COGs. Over 40% were found to co-evolve with at least one partner. We partitioned the network of co-evolutionary relations into clusters and uncovered multiple modular assemblies of genes with clearly defined functions. Finally, we measured the extent to which co-evolutionary relations coincide with other cellular relations such as genomic proximity, gene fusion propensity, co-expression, protein-protein interactions and metabolic connections. Our results show that co-evolutionary relations only partially overlap with these other types of networks. Our results suggest that the inferred co-evolutionary network in prokaryotes is highly informative towards revealing functional relations among genes, often showing signals that cannot be extracted from other network types. AVAILABILITY AND IMPLEMENTATION: Available under GPL license as open source. CONTACT: talp@post.tau.ac.il. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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