ArticleScientific reports2019
Patterns of diverse gene functions in genomic neighborhoods predict gene function and phenotype.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 28 citations in OpenAlex.
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- Systematic analysis of the underlying genomic architecture for transcriptional-translational coupling in prokaryotes.NAR genomics and bioinformatics · 2022Article
- Gene function prediction in five model eukaryotes exclusively based on gene relative location through machine learning.Scientific reports · 2022Article
- Lysophosphatidic acid receptor 6 regulated by miR-27a-3p attenuates tumor proliferation in breast cancer.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2022Article
- The Moderately (D)efficient Enzyme: Catalysis-Related DamageBiochemistry · 2021Article
- Using CRISPR to understand and manipulate gene regulation.Development (Cambridge, England) · 2021Review
- Underpinning the molecular programming attributing heat stress associated thermotolerance in tea (Camellia sinensis (L.) O. Kuntze).Horticulture research · 2021Article
- Colocality to Cofunctionality: Eukaryotic Gene Neighborhoods as a Resource for Function Discovery.Molecular biology and evolution · 2021Article
- cblaster: a remote search tool for rapid identification and visualization of homologous gene clusters.Bioinformatics advances · 2021Article
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Authors and funding
3 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genes with similar roles in the cell cluster on chromosomes, thus benefiting from coordinated regulation. This allows gene function to be inferred by transferring annotations from genomic neighbors, following the guilt-by-association principle. We performed a systematic search for co-occurrence of >1000 gene functions in genomic neighborhoods across 1669 prokaryotic, 49 fungal and 80 metazoan genomes, revealing prevalent patterns that cannot be explained by clustering of functionally similar genes. It is a very common occurrence that pairs of dissimilar gene functions - corresponding to semantically distant Gene Ontology terms - are significantly co-located on chromosomes. These neighborhood associations are often as conserved across genomes as the known associations between similar functions, suggesting selective benefits from clustering of certain diverse functions, which may conceivably play complementary roles in the cell. We propose a simple encoding of chromosomal gene order, the neighborhood function profiles (NFP), which draws on diverse gene clustering patterns to predict gene function and phenotype. NFPs yield a 26-46% increase in predictive power over state-of-the-art approaches that propagate function across neighborhoods, thus providing hundreds of novel, high-confidence gene function inferences per genome. Furthermore, we demonstrate that copy number-neutral structural variation that shapes gene function distribution across chromosomes can predict phenotype of individuals from their genome sequence.
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