ArticlePLoS computational biology2013
Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 40 citations in OpenAlex.
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- Role of the LuxR solo, SdiA, in eavesdropping on foreign bacteria.FEMS microbiology reviews · 2025Review
- Assembling bacterial puzzles: piecing together functions into microbial pathways.NAR genomics and bioinformatics · 2024Article
- Interrogation of RNA-protein interaction dynamics in bacterial growth.Molecular systems biology · 2024Article
- FinO/ProQ-family proteins: an evolutionary perspective.Bioscience reports · 2023Review
- The minimal meningococcal ProQ protein has an intrinsic capacity for structure-based global RNA recognition.Nature communications · 2020Article
- Identifying orthologs with OMA: A primer.F1000Research · 2020Article
- Combining learning and constraints for genome-wide protein annotation.BMC bioinformatics · 2019Article
- Quantifying changes in the bacterial thiol redox proteome during host-pathogen interaction.Redox biology · 2019Article
- The evolutionary signal in metagenome phyletic profiles predicts many gene functions.Microbiome · 2018Article
- Molecular mechanism of mRNA repression inThe EMBO journal · 2017Article
- Metabolic Pathway Assignment of Plant Genes based on Phylogenetic Profiling-A Feasibility Study.Frontiers in plant science · 2017Article
- Combining Shigella Tn-seq data with gold-standard E. coli gene deletion data suggests rare transitions between essential and non-essential gene functionality.BMC microbiology · 2016Article
- The Code of Silence: Widespread Associations Between Synonymous Codon Biases and Gene Function.Journal of molecular evolution · 2016Review
- Gene expression profiles of wild-type and isoniazid-resistant strains of Mycobacterium smegmatis.Data in brief · 2015Article
- Global Shifts in Genome and Proteome Composition Are Very Tightly Coupled.Genome biology and evolution · 2015Article
- Enrichment of Triticum aestivum gene annotations using ortholog cliques and gene ontologies in other plants.BMC genomics · 2015Article
- The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements.Nucleic acids research · 2015Article
- Phylogenetic profiling: how much input data is enough?PloS one · 2015Article
- Inferring gene function from evolutionary change in signatures of translation efficiency.Genome biology · 2014Article
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
New microbial genomes are sequenced at a high pace, allowing insight into the genetics of not only cultured microbes, but a wide range of metagenomic collections such as the human microbiome. To understand the deluge of genomic data we face, computational approaches for gene functional annotation are invaluable. We introduce a novel model for computational annotation that refines two established concepts: annotation based on homology and annotation based on phyletic profiling. The phyletic profiling-based model that includes both inferred orthologs and paralogs-homologs separated by a speciation and a duplication event, respectively-provides more annotations at the same average Precision than the model that includes only inferred orthologs. For experimental validation, we selected 38 poorly annotated Escherichia coli genes for which the model assigned one of three GO terms with high confidence: involvement in DNA repair, protein translation, or cell wall synthesis. Results of antibiotic stress survival assays on E. coli knockout mutants showed high agreement with our model's estimates of accuracy: out of 38 predictions obtained at the reported Precision of 60%, we confirmed 25 predictions, indicating that our confidence estimates can be used to make informed decisions on experimental validation. Our work will contribute to making experimental validation of computational predictions more approachable, both in cost and time. Our predictions for 998 prokaryotic genomes include ~400000 specific annotations with the estimated Precision of 90%, ~19000 of which are highly specific-e.g. "penicillin binding," "tRNA aminoacylation for protein translation," or "pathogenesis"-and are freely available at http://gorbi.irb.hr/.
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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.