ArticleCell reports2015
Systematic Discovery of Human Gene Function and Principles of Modular Organization through Phylogenetic Profiling.
Article in Cell reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Computational strategies for cross-species knowledge transfer.Nature methods · 2026Review
- CORGIAS: identifying correlated gene pairs by considering evolutionary history in a large-scale prokaryotic genome dataset.NAR genomics and bioinformatics · 2025Article
- Profylo: A Python Package for Phylogenetic Profile Comparison and Analysis.Journal of molecular evolution · 2025Article
- Autophagy inhibition in intestinal stem cells favors enteroendocrine cell differentiation through Stat92E activity.Disease models & mechanisms · 2025Article
- Barcode sequencing: a robust, platform-agnostic method for massively parallel cell-based screens.G3 (Bethesda, Md.) · 2025Article
- C11orf54 catalyzes L-xylulose formation in human metabolism.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- ProTaxoVis-protein taxonomic visualisation of presence.BMC bioinformatics · 2025Article
- Computational strategies for cross-species knowledge transfer and translational biomedicine.ArXiv · 2024Article
- Structure and interactions of the endogenous human Commander complex.Nature structural & molecular biology · 2024Article
- Using multi-scale genomics to associate poorly annotated genes with rare diseases.Genome medicine · 2024Article
- Metabolomics and lipidomics strategies in modern drug discovery and development.Drug discovery today · 2023Review
- A phylogenetic profiling approach identifies novel ciliogenesis genes in Drosophila and C. elegans.The EMBO journal · 2023Article
- Prioritization and functional validation of target genes from single-cell transcriptomics studies.Communications biology · 2023Article
- Article
- Phylogenetic profiling in eukaryotes comes of age.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Identification of hidden associations among eukaryotic genes through statistical analysis of coevolutionary transitions.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- A CUG-initiated CATSPERθ functions in the CatSper channel assembly and serves as a checkpoint for flagellar trafficking.bioRxiv : the preprint server for biology · 2023Article
- Defining characteristics and conservation of poorly annotated genes in Caenorhabditis elegans using WormCat 2.0.Genetics · 2022Article
- Evolutionary rewiring of regulatory networks contributes to phenotypic differences between human and mouse orthologous genes.Nucleic acids research · 2022Article
- Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Functional links between genes can be predicted using phylogenetic profiling, by correlating the appearance and loss of homologs in subsets of species. However, effective genome-wide phylogenetic profiling has been hindered by the large fraction of human genes related to each other through historical duplication events. Here, we overcame this challenge by automatically profiling over 30,000 groups of homologous human genes (orthogroups) representing the entire protein-coding genome across 177 eukaryotic species (hOP profiles). By generating a full pairwise orthogroup phylogenetic co-occurrence matrix, we derive unbiased genome-wide predictions of functional modules (hOP modules). Our approach predicts functions for hundreds of poorly characterized genes. The results suggest evolutionary constraints that lead components of protein complexes and metabolic pathways to co-evolve while genes in signaling and transcriptional networks do not. As a proof of principle, we validated two subsets of candidates experimentally for their predicted link to the actin-nucleating WASH complex and cilia/basal body function.
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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.