Gephebase, a database of genotype–phenotype relationships for natural and domesticated variation in Eukaryotes

• Published in: Nucleic acids research Vol. 48; no. D1; pp. D696 - D703
• Main Authors: Courtier-Orgogozo, Virginie, Arnoult, Laurent, Prigent, Stéphane R, Wiltgen, Séverine, Martin, Arnaud
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 08.01.2020
• Subjects: Algorithms; Alleles; Animal genetics; Animals; Biodiversity; Chromosome Mapping; Computational Biology - methods; Computer Graphics; Database Issue; Databases, Factual; Databases, Genetic; DNA Transposable Elements; Drosophila melanogaster; Eukaryota - genetics; Genetic Association Studies; Genetic Linkage; Genetics; Humans; Internet; Life Sciences; Mutation; Populations and Evolution; Software; User-Computer Interface
• ISSN: 0305-1048; 1362-4962; 1362-4954; 1362-4962
• DOI: 10.1093/nar/gkz796

Abstract Gephebase is a manually-curated database compiling our accumulated knowledge of the genes and mutations that underlie natural, domesticated and experimental phenotypic variation in all Eukaryotes—mostly animals, plants and yeasts. Gephebase aims to compile studies where the genotype–phenotype association (based on linkage mapping, association mapping or a candidate gene approach) is relatively well supported. Human clinical traits and aberrant mutant phenotypes in laboratory organisms are not included and can be found in other databases (e.g. OMIM, OMIA, Monarch Initiative). Gephebase contains more than 1700 entries. Each entry corresponds to an allelic difference at a given gene and its associated phenotypic change(s) between two species or two individuals of the same species, and is enriched with molecular details, taxonomic information, and bibliographic information. Users can easily browse entries and perform searches at various levels using boolean operators (e.g. transposable elements, snakes, carotenoid content, Doebley). Data is exportable in spreadsheet format. This database allows to perform meta-analyses to extract global trends about the living world and the research fields. Gephebase should also help breeders, conservationists and others to identify promising target genes for crop improvement, parasite/pest control, bioconservation and genetic diagnostic. It is freely available at www.gephebase.org.