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Import HGNC data

Source: R/import_hgnc_dataset.R
import_hgnc_dataset.Rd

This function imports into memory, as a tibble, the complete HGNC data set from a TSV file.

Usage

import_hgnc_dataset(file = latest_archive_url(), ...)

Arguments

file

A file or URL of the complete HGNC data set (in TSV format).

...

Additional arguments to be passed on to readr::read_tsv().

Value

A tibble of the HGNC data set consisting of 55 columns:

hgnc_id

A unique ID provided by the HGNC for each gene with an approved symbol. IDs are of the format HGNC:n, where n is a unique number. HGNC IDs remain stable even if a name or symbol changes.

hgnc_id2

A stripped down version of hgnc_id where the prefix "HGNC:" has been removed (this column is added by the package {hgnc}).

symbol

The official gene symbol approved by the HGNC, which is typically a short form of the gene name. Symbols are approved in accordance with the Guidelines for Human Gene Nomenclature.

name

The full gene name approved by the HGNC; corresponds to the approved symbol above.

locus_group

A group name for a set of related locus types as defined by the HGNC. One of: "protein-coding gene", "non-coding RNA", "pseudogene" or "other".

locus_type

Specifies the genetic class of each gene entry:

"gene with protein product"

Protein-coding genes (the protein may be predicted and of unknown function), SO:0001217.

"RNA, cluster"

Region containing a cluster of small non-coding RNA genes.

"RNA, long non-coding"

Non-protein coding genes that encode long non-coding RNAs (lncRNAs) SO:0001877; these are at least 200 nt in length. Subtypes include intergenic SO:0001463, intronic SO:0001903 and antisense SO:0001904.

"RNA, micro"

Non-protein coding genes that encode microRNAs (miRNAs), SO:0001265.

"RNA, ribosomal"

Non-protein coding genes that encode ribosomal RNAs (rRNAs), SO:0001637.

"RNA, small nuclear"

Non-protein coding genes that encode small nuclear RNAs (snRNAs), SO:0001268.

"RNA, small nucleolar"

Non-protein coding genes that encode small nucleolar RNAs (snoRNAs) containing C/D or H/ACA box domains, SO:0001267.

"RNA, small cytoplasmic"

Non-protein coding genes that encode small cytoplasmic RNAs (scRNAs), SO:0001266.

"RNA, transfer"

Non-protein coding genes that encode transfer RNAs (tRNAs), SO:0001272.

"RNA, small misc"

Non-protein coding genes that encode miscellaneous types of small ncRNAs, such as vault (SO:0000404) and Y (SO:0000405) RNA genes.

"phenotype only"

Mapped phenotypes where the causative gene has not been identified, SO:0001500.

"pseudogene"

Genomic DNA sequences that are similar to protein-coding genes but do not encode a functional protein, SO:0000336.

"complex locus constituent"

Transcriptional unit that is part of a named complex locus.

"endogenous retrovirus"

Integrated retroviral elements that are transmitted through the germline, SO:0000100.

"fragile site"

A heritable locus on a chromosome that is prone to DNA breakage.

"immunoglobulin gene"

Gene segments that undergo somatic recombination to form heavy or light chain immunoglobulin genes (SO:0000460). Also includes immunoglobulin gene segments with open reading frames that either cannot undergo somatic recombination, or encode a peptide that is not predicted to fold correctly; these are identified by inclusion of the term "non-functional" in the gene name.

"immunoglobulin pseudogene"

Immunoglobulin gene segments that are inactivated due to frameshift mutations and/or stop codons in the open reading frame.

"protocadherin"

Gene segments that constitute the three clustered protocadherins (alpha, beta and gamma)

"readthrough"

A naturally occurring transcript containing coding sequence from two or more genes that can also be transcribed individually.

"region"

Extents of genomic sequence that contain one or more genes, also applied to non-gene areas that do not fall into other types.

"T cell receptor gene"

Gene segments that undergo somatic recombination to form either alpha, beta, gamma or delta chain T cell receptor genes (SO:0000460). Also includes T cell receptor gene segments with open reading frames that either cannot undergo somatic recombination, or encode a peptide that is not predicted to fold correctly; these are identified by inclusion of the term "non-functional" in the gene name.

"T cell receptor pseudogene"

T cell receptor gene segments that are inactivated due to frameshift mutations and/or stop codons in the open reading frame.

"transposable element"

A segment of repetitive DNA that can move, or retrotranspose, to new sites within the genome (SO:0000101).

"unknown"

Entries where the locus type is currently unknown.

"virus integration site"

Target sequence for the integration of viral DNA into the genome.

status

Status of the symbol report, which can be either "Approved" or "Entry Withdrawn".

location

Chromosomal location. Indicates the cytogenetic location of the gene or region on the chromsome, e.g. "19q13.43". In the absence of that information one of the following may be listed:

"not on reference assembly"

Named gene is not annotated on the current version of the Genome Reference Consortium human reference assembly; may have been annotated on previous assembly versions or on a non-reference human assembly.

"unplaced"

Named gene is annotated on an unplaced/unlocalized scaffold of the human reference assembly.

"reserved"

Named gene has never been annotated on any human assembly.

location_sortable

A sortable version of the location column (see above).

alias_symbol

Alternative symbols that have been used to refer to the gene. Aliases may be from literature, from other databases or may be added to represent membership of a gene group.

alias_name

Alternative names for the gene. Aliases may be from literature, from other databases or may be added to represent membership of a gene group.

prev_symbol

This field displays any symbols that were previously HGNC-approved nomenclature.

prev_name

This field displays any names that were previously HGNC-approved nomenclature.

gene_group

A gene group. Each gene has been assigned to one or more groups, according to either sequence similarity or information from publications, specialist advisors for that group or other databases. Groups may be either structural or functional.

gene_group_id

Gene group identifier, an integer number. This column contains the gene group identifiers, see gene_group for the gene group name.

date_approved_reserved

The date the entry was first approved.

date_symbol_changed

The date the gene symbol was last changed.

date_name_changed

The date the gene name was last changed.

date_modified

Date the entry was last modified.

entrez_id

Entrez gene identifier.

ensembl_gene_id

Ensembl gene identifier.

vega_id

VEGA gene identifier.

ucsc_id

UCSC gene identifier.

ena

International Nucleotide Sequence Database Collaboration (GenBank, ENA and DDBJ) accession number(s).

refseq_accession

The Reference Sequence (RefSeq) identifier for that entry, provided by the NCBI.

ccds_id

Consensus CDS identifier.

uniprot_ids

UniProt protein accession.

pubmed_id

Pubmed and Europe Pubmed Central PMIDs.

mgd_id

Mouse genome informatics database identifier.

rgd_id

Rat genome database gene identifier.

lsdb

The name of the Locus Specific Mutation Database and URL for the gene.

cosmic

Symbol used within the Catalogue of somatic mutations in cancer for the gene.

omim_id

Online Mendelian Inheritance in Man (OMIM) identifier.

mirbase

miRBase identifier.

homeodb

Homeobox Database identifier.

snornabase

snoRNABase identifier.

bioparadigms_slc

Symbol used to link to the SLC tables database at bioparadigms.org for the gene.

orphanet

Orphanet identifier.

pseudogene.org

Pseudogene.org identifier.

horde_id

Symbol used within HORDE for the gene.

merops

Identifier used to link to the MEROPS peptidase database.

imgt

Symbol used within international ImMunoGeneTics information system.

iuphar

The objectId used to link to the IUPHAR/BPS Guide to PHARMACOLOGY database.

kznf_gene_catalog

Lawrence Livermore National Laboratory Human KZNF Gene Catalog (LLNL) identifier.

mamit-trnadb

Identifier to link to the Mamit-tRNA database.

cd

Symbol used within the Human Cell Differentiation Molecule database for the gene.

lncrnadb

lncRNA Database identifier.

enzyme_id

ENZYME EC accession number.

intermediate_filament_db

Identifier used to link to the Human Intermediate Filament Database.

rna_central_ids

Identifier in the RNAcentral, The non-coding RNA sequence database.

lncipedia

The LNCipedia identifier to which the gene belongs. This will only appear if the gene is a long non-coding RNA.

gtrnadb

The GtRNAdb identifier to which the gene belongs. This will only appear if the gene is a tRNA.

agr

The Alliance of Genomic Resources HGNC ID for the Human gene page within the resource.

mane_select

MANE Select nucleotide accession with version (i.e. NCBI RefSeq or Ensembl transcript ID and version).

gencc

Gene Curation Coalition (GenCC) Database identifier.

Examples

if (FALSE) import_hgnc_dataset()