ReviewJournal of the Royal Society, Interface2008
Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution.
Review in Journal of the Royal Society, Interface, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed.
- ProTaxoVis-protein taxonomic visualisation of presence.BMC bioinformatics · 2025Article
- Phylogenetic Profiling Analysis of the Phycobilisome Revealed a Novel State-Transition Regulator Gene in Synechocystis sp. PCC 6803.Plant & cell physiology · 2024Article
- Assembling bacterial puzzles: piecing together functions into microbial pathways.NAR genomics and bioinformatics · 2024Article
- ncOrtho: efficient and reliable identification of miRNA orthologs.Nucleic acids research · 2023Article
- Inverse Potts model improves accuracy of phylogenetic profiling.Bioinformatics (Oxford, England) · 2022Article
- Co-evolution based machine-learning for predicting functional interactions between human genes.Nature communications · 2021Article
- CladeOScope: functional interactions through the prism of clade-wise co-evolution.NAR genomics and bioinformatics · 2021Article
- Novel metric for hyperbolic phylogenetic tree embeddings.Biology methods & protocols · 2021Article
- Mirage: estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families.Bioinformatics advances · 2021Article
- Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes.PLoS computational biology · 2020Article
- Logicome Profiler: Exhaustive detection of statistically significant logic relationships from comparative omics data.PloS one · 2020Article
- Measuring the impact of gene prediction on gene loss estimates in Eukaryotes by quantifying falsely inferred absences.PLoS computational biology · 2019Article
- A Genome-Scale Co-Functional Network ofMolecules and cells · 2019Article
- Article
- The evolutionary signal in metagenome phyletic profiles predicts many gene functions.Microbiome · 2018Article
- Modules of co-occurrence in the cyanobacterial pan-genome reveal functional associations between groups of ortholog genes.PLoS genetics · 2018Article
- Phylogenetic Profiling of Mitochondrial Proteins and Integration Analysis of Bacterial Transcription Units Suggest Evolution of F1Fo ATP Synthase from Multiple Modules.Journal of molecular evolution · 2017Article
- Phylo_dCor: distance correlation as a novel metric for phylogenetic profiling.BMC bioinformatics · 2017Article
- Evolutionary dynamics of the kinetochore network in eukaryotes as revealed by comparative genomics.EMBO reports · 2017Article
- Unique Phylogenetic Distributions of the Ska and Dam1 Complexes Support Functional Analogy and Suggest Multiple Parallel Displacements of Ska by Dam1.Genome biology and evolution · 2017Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The gap between the amount of genome information released by genome sequencing projects and our knowledge about the proteins' functions is rapidly increasing. To fill this gap, various 'genomic-context' methods have been proposed that exploit sequenced genomes to predict the functions of the encoded proteins. One class of methods, phylogenetic profiling, predicts protein function by correlating the phylogenetic distribution of genes with that of other genes or phenotypic characteristics. The functions of a number of proteins, including ones of medical relevance, have thus been predicted and subsequently confirmed experimentally. Additionally, various approaches to measure the similarity of phylogenetic profiles and to account for the phylogenetic bias in the data have been proposed. We review the successful applications of phylogenetic profiling and analyse the performance of various profile similarity measures with a set of one microsporidial and 25 fungal genomes. In the fungi, phylogenetic profiling yields high-confidence predictions for the highest and only the highest scoring gene pairs illustrating both the power and the limitations of the approach. Both practical examples and theoretical considerations suggest that in order to get a reliable and specific picture of a protein's function, results from phylogenetic profiling have to be combined with other sources of evidence.
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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.