Guidelines for human gene nomenclature

Bruford, Elspeth A.; Braschi, Bryony; Denny, Paul; Jones, Tamsin E. M.; Seal, Ruth L.; Tweedie, Susan

doi:10.1038/s41588-020-0669-3

Cited by 151 publications

(136 citation statements)

References 22 publications

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“…Changes to gene symbols can be disruptive and cause confusion, and in the case of genes associated with disease could even result in an incorrect diagnosis and treatment. Consequently, our symbol updates are now limited and occur only in scenarios where the benefits of change clearly outweigh the disadvantages ( 1 ). In an effort to provide additional stability for genes associated with disease, we have been reviewing their nomenclature and marking them with the tag ‘stable symbol’ when we are confident that future symbol changes are extremely unlikely.…”

Section: Hgnc Datamentioning

confidence: 99%

“…We name protein-coding genes, genes encoding RNA and pseudogenes; we do not name alleles and we no longer name phenotypes. We have recently published our updated naming guidelines ( 1 ), which reflect changes in policy in recent years and emphasise our aim to keep gene symbols stable where possible. We have also published a detailed set of guidelines specifically for naming RNA genes ( 2 ).…”

Section: Introductionmentioning

confidence: 99%

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Genenames.org: the HGNC and VGNC resources in 2021

Tweedie

Braschi

Gray

et al. 2020

Nucleic Acids Research

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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 42,000 approved gene symbols in our current database of which over 19 000 are for protein-coding genes. While we still update placeholder and problematic symbols, we are working towards stabilizing symbols where possible; over 2000 symbols for disease associated genes are now marked as stable in our symbol reports. All of our data is available at the HGNC website https://www.genenames.org. The Vertebrate Gene Nomenclature Committee (VGNC) was established to assign standardized nomenclature in line with human for vertebrate species lacking their own nomenclature committee. In addition to the previous VGNC core species of chimpanzee, cow, horse and dog, we now name genes in cat, macaque and pig. Gene groups have been added to VGNC and currently include two complex families: olfactory receptors (ORs) and cytochrome P450s (CYPs). In collaboration with specialists we have also named CYPs in species beyond our core set. All VGNC data is available at https://vertebrate.genenames.org/. This article provides an overview of our online data and resources, focusing on updates over the last two years.

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Section: Hgnc Datamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genenames.org: the HGNC and VGNC resources in 2021

Tweedie

Braschi

Gray

et al. 2020

Nucleic Acids Research

Self Cite

300

262

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“…For peptide-encoded lncRNAs, we extracted the names, sequences and lengths of the encoded peptides. Each entry was curated and checked by at least two specialists and proofread non-standard names of lncRNAs according to the HUGO Gene Nomenclature Committee (HGNC) ( 35 ). Sequence and position information of lncRNAs were annotated according to NCBI with links pointing to accessions in the NCBI ( 20 ) and Ensembl ( 36 ) provided if known.…”

Section: Data Collectionmentioning

confidence: 99%

EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments

Zhou

Liu

et al. 2020

Nucleic Acids Research

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Long non-coding RNAs (lncRNAs) play important functional roles in many diverse biological processes. However, not all expressed lncRNAs are functional. Thus, it is necessary to manually collect all experimentally validated functional lncRNAs (EVlncRNA) with their sequences, structures, and functions annotated in a central database. The first release of such a database (EVLncRNAs) was made using the literature prior to 1 May 2016. Since then (till 15 May 2020), 19 245 articles related to lncRNAs have been published. In EVLncRNAs 2.0, these articles were manually examined for a major expansion of the data collected. Specifically, the number of annotated EVlncRNAs, associated diseases, lncRNA-disease associations, and interaction records were increased by 260%, 320%, 484% and 537%, respectively. Moreover, the database has added several new categories: 8 lncRNA structures, 33 exosomal lncRNAs, 188 circular RNAs, and 1079 drug-resistant, chemoresistant, and stress-resistant lncRNAs. All records have checked against known retraction and fake articles. This release also comes with a highly interactive visual interaction network that facilitates users to track the underlying relations among lncRNAs, miRNAs, proteins, genes and other functional elements. Furthermore, it provides links to four new bioinformatics tools with improved data browsing and searching functionality. EVLncRNAs 2.0 is freely available at https://www.sdklab-biophysics-dzu.net/EVLncRNAs2/.

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“…The FAM230 lincRNA and FAM247 lincRNA gene families were named by the HUGO Gene Nomenclature Committee (https://www.genenames.org/) [14]. These genes exemplify how segmental duplications or low copy repeats in chromosome 22 are a driving element in the genesis and proliferation of lincRNA gene families.…”

Section: Lincrna Gene Familiesmentioning

confidence: 99%

Genesis of Non-Coding RNA Genes in Human Chromosome 22—A Sequence Connection with Protein Genes Separated by Evolutionary Time

Delihas

2020

ncRNA

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A small phylogenetically conserved sequence of 11,231 bp, termed FAM247, is repeated in human chromosome 22 by segmental duplications. This sequence forms part of diverse genes that span evolutionary time, the protein genes being the earliest as they are present in zebrafish and/or mice genomes, and the long noncoding RNA genes and pseudogenes the most recent as they appear to be present only in the human genome. We propose that the conserved sequence provides a nucleation site for new gene development at evolutionarily conserved chromosomal loci where the FAM247 sequences reside. The FAM247 sequence also carries information in its open reading frames that provides protein exon amino acid sequences; one exon plays an integral role in immune system regulation, specifically, the function of ubiquitin-specific protease (USP18) in the regulation of interferon. An analysis of this multifaceted sequence and the genesis of genes that contain it is presented.

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Guidelines for human gene nomenclature

Cited by 151 publications

References 22 publications

Genenames.org: the HGNC and VGNC resources in 2021

Genenames.org: the HGNC and VGNC resources in 2021

EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments

Genesis of Non-Coding RNA Genes in Human Chromosome 22—A Sequence Connection with Protein Genes Separated by Evolutionary Time

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