Genenames.org: the HGNC and VGNC resources in 2019

By Bryony Braschi, Paul Denny, Kristian A. Gray, T. Jones, Ruth L. Seal, S. Tweedie, Bethan Yates, E. Bruford. 2018

289 citations recorded by the source corpus.

Abstract The HUGO Gene Nomenclature Committee (HGNC) based at EMBL’s European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. There are over 40 000 approved gene symbols in our current database of which over 19 000 are for protein-coding genes. The Vertebrate Gene Nomenclature Committee (VGNC) was established in 2016 to assign standardized nomenclature in line with human for vertebrate species that lack their own nomenclature committees. The VGNC initially assigned nomenclature for over 15000 protein-coding genes in chimpanzee. We have extended this process to other vertebrate species, naming over 14000 protein-coding genes in cow and dog and over 13 000 in horse to date. Our HGNC website https://www.genenames.org has undergone a major design update, simplifying the homepage to provide easy access to our search tools and making the site more mobile friendly. Our gene families pages are now known as ‘gene groups’ and have increased in number to over 1200, with nearly half of all named genes currently assigned to at least one gene group. This article provides an overview of our online data and resources, focusing on our work over the last two years.

Subfields: Molecular Biology

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Citations in the corpus

OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more (2020, neutral): “Conversely, OMA orthologs are integrated by various resources, including UniProt, HGNC/VGNC, GenBank (15), the Alliance of Genome Resources (16), and Bgee (17).”
FlyBase: updates to the Drosophila melanogaster knowledge base (2020, unknown): “Similar to the Pathway Reports described above, these reports tabulate the members of specific enzyme groups, alongside key relevant GO terms, source references and external resources, including equivalent human enzyme groups (13).”
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases (2020, background): “The HGNC has also increased its small nuclear RNA dataset by 13% and its transfer RNA dataset by 2.5%.”
Genenames.org: the HGNC and VGNC resources in 2021 (2020, methodology): “We describe the changes made to the HGNC and VGNC resources since our last report in 2019 (23).”
The UCSC Genome Browser database: 2021 update (2020, methodology): “These tracks represent experimentally validated promoters based on gene transcript models obtained from multiple sources (HGNC (30), GENCODE (31), Ensembl (32) and RefSeq (33)), then validated using data from CAGE (34) and RAMPAGE (35) experimental studies obtained from FANTOM 5 (36), UCSC, and ENCO”