Genenames.org: the HGNC and VGNC resources in 2017

By Bethan Yates, Bryony Braschi, Kristian A. Gray, Ruth L. Seal, S. Tweedie, E. Bruford. Nucleic Acids Res., 2016

330 citations recorded by the source corpus.

The HUGO Gene Nomenclature Committee (HGNC) based at the European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. Currently the HGNC database contains almost 40 000 approved gene symbols, over 19 000 of which represent protein-coding genes. In addition to naming genomic loci we manually curate genes into family sets based on shared characteristics such as homology, function or phenotype. We have recently updated our gene family resources and introduced new improved visualizations which can be seen alongside our gene symbol reports on our primary website http://www.genenames.org. In 2016 we expanded our remit and formed the Vertebrate Gene Nomenclature Committee (VGNC) which is responsible for assigning names to vertebrate species lacking a dedicated nomenclature group. Using the chimpanzee genome as a pilot project we have approved symbols and names for over 14 500 protein-coding genes in chimpanzee, and have developed a new website http://vertebrate.genenames.org to distribute these data. Here, we review our online data and resources, focusing particularly on the improvements and new developments made during the last two years.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e50fe9113331bdb5bd2ddc07d50dbb42fe12102d

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Citations in the corpus

PubChem 2019 update: improved access to chemical data (2018, background): “These annotations are collected from major molecular biology databases, including NCBI Gene (12), Gene Ontology (13,14), Human Genome Organization (HUGO) Gene Nomenclature Committee (HGNC) (15), UniProt (16), Protein Data Bank (PDB) (17), Conserved Domains Database (CDD) (18), Pfam (19), MedGen (20)”
Genenames.org: the HGNC and VGNC resources in 2021 (2020, background): “Our younger sister project, the Vertebrate Gene Nomenclature committee, is now in its 5th year of naming genes in selected vertebrate species that do not have their own dedicated nomenclature committee (20).”
Cellular and inter-cellular rewiring of the human colon during ulcerative colitis (2019, methodology): “Human pattern recognition receptors were obtained from PRRDB (Lata and Raghava, 2008) and supplemented with Human Gene Nomenclature Committee (HGNC) “C-type lectin domain containing” gene family members (Yates et al., 2017).”
ClinVar: improving access to variant interpretations and supporting evidence (2017, background): “(ii) Variants in specific genes may be searched by HGNC IDs (11), as well as by GeneIDs (5), e.”
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces (2017, positive): “Whenever available, we use the gene name established by the HUGO gene nomenclature committee (38).”
A Human IgSF Cell-Surface Interactome Reveals a Complex Network of Protein-Protein Interactions (2020, methodology): “Selection and Production of Proteins for PPI Screening To identify human IgSF proteins, we utilized the HUGO Gene Nomenclature Committee (HGNC) (Yates et al., 2017), Human Protein Atlas (Uhlén et al.”
Exploration of prognosis-related microRNA and transcription factor co-regulatory networks across cancer types (2019, methodology): “We unified TF/miRNA/ target gene symbols in the regulatory relationship by referring the Hugo Gene Nomenclature Committee (HGNC) [66], the approval TF list [67,68], and miRBase [69].”
COSMIC: the Catalogue Of Somatic Mutations In Cancer (2018, background): “The first phase, which is currently underway, is to upgrade the annotation system and data model, which will facilitate still closer interoperability with external resources such as Ensembl (15), HGNC (16) and RefSeq (17), and with the increasing number of analytical and visualization systems in dev”
RNAcentral: a hub of information for non-coding RNA sequences (2018, neutral): “Additionally, we have imported ncRNA data from Ensembl (6), GENCODE (17), HGNC (HUGO Gene Nomenclature Committee) (18), and TarBase (19).”
Genenames.org: the HGNC and VGNC resources in 2019 (2018, methodology): “We established the Vertebrate Gene Nomenclature Committee (VGNC) in 2016 to assign standardized nomenclature in line with human for vertebrate species that lack their own nomenclature committees (11).”
The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY (2017, neutral): “org/cgi-bin/genefamilies/) (15,16); examples include cytokines and chemokines.”
LNCipedia 5: towards a reference set of human long non-coding RNAs (2018, methodology): “As the number of lncRNAs with a gene symbol provided by the HUGO Gene Nomenclature Committee (HGNC) has grown substantially (26), LNCipedia 5 now uses a hybrid solution for gene names.”
ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments (2017, methodology): “org, (6,7)), ReMap meta-data for each experiment are manually curated, annotated with the official gene name from the HUGO Gene Nomenclature Committee (8) (www.”