Import Human Genome Organization (HUGO) Gene Nomenclature Committee (HGNC) metadata
Source:R/Hgnc.R
Hgnc.RdImport Human Genome Organization (HUGO) Gene Nomenclature Committee (HGNC) metadata
Examples
object <- Hgnc()
#> → Importing HGNC complete set.
#> → Importing /Users/mike/.cache/R/AcidGenomes/BiocFileCache/886a796ea9b4_hgnc_complete_set.txt using base::`readLines()`.
#> → Importing text connection with base::`read.table()`.
print(object)
#> Hgnc with 43736 rows and 52 columns
#> hgncId geneName description locusGroup
#> <integer> <character> <character> <character>
#> 5 5 A1BG alpha-1-B glycoprotein protein-coding gene
#> 7 7 A2M alpha-2-macroglobulin protein-coding gene
#> 8 8 A2MP1 alpha-2-macroglobuli.. pseudogene
#> 15 15 NATP N-acetyltransferase .. pseudogene
#> 16 16 SERPINA3 serpin family A memb.. protein-coding gene
#> ... ... ... ... ...
#> 56900 56900 IDH1P1 IDH1 pseudogene 1 pseudogene
#> 56902 56902 ESDP1 ESD pseudogene 1 pseudogene
#> 56903 56903 NGRNP4 NGRN pseudogene 4 pseudogene
#> 56904 56904 ISG20L2P1 ISG20L2 pseudogene 1 pseudogene
#> 56905 56905 ISG20L2P2 ISG20L2 pseudogene 2 pseudogene
#> locusType status location locationSortable
#> <character> <character> <character> <character>
#> 5 gene with protein pr.. Approved 19q13.43 19q13.43
#> 7 gene with protein pr.. Approved 12p13.31 12p13.31
#> 8 pseudogene Approved 12p13.31 12p13.31
#> 15 pseudogene Approved 8p22 08p22
#> 16 gene with protein pr.. Approved 14q32.13 14q32.13
#> ... ... ... ... ...
#> 56900 pseudogene Approved 6p24.3 06p24.3
#> 56902 pseudogene Approved 6p22.3 06p22.3
#> 56903 pseudogene Approved 6p22.3 06p22.3
#> 56904 pseudogene Approved 6p22.3 06p22.3
#> 56905 pseudogene Approved 11q23.2 11q23.2
#> aliasSymbol aliasName prevSymbol
#> <CharacterList> <CharacterList> <CharacterList>
#> 5 NA NA NA
#> 7 FWP007,S863-7,CPAMD5 NA NA
#> 8 NA NA A2MP
#> 15 NATP1 NA AACP
#> 16 ACT alpha-1 antichymotry.. AACT
#> ... ... ... ...
#> 56900 NA NA NA
#> 56902 NA NA NA
#> 56903 NA NA NA
#> 56904 NA NA NA
#> 56905 NA NA NA
#> prevName
#> <CharacterList>
#> 5 NA
#> 7 NA
#> 8 alpha-2-macroglobuli..
#> 15 arylamide acetylase ..
#> 16 alpha-1-antichymotry..,serine (or cysteine)..,serpin peptidase inh..
#> ... ...
#> 56900 NA
#> 56902 NA
#> 56903 NA
#> 56904 NA
#> 56905 NA
#> geneGroup geneGroupId dateApprovedReserved
#> <CharacterList> <CharacterList> <Date>
#> 5 Immunoglobulin like .. 594 1989-06-30
#> 7 Alpha-2-macroglobuli.. 2148 1986-01-01
#> 8 NA NA 1991-09-12
#> 15 Arylamine N-acetyltr.. 1133 1992-07-09
#> 16 Serpin peptidase inh.. 739 2001-06-22
#> ... ... ... ...
#> 56900 NA NA 2023-09-14
#> 56902 NA NA 2023-09-14
#> 56903 NA NA 2023-09-14
#> 56904 NA NA 2023-09-14
#> 56905 NA NA 2023-09-14
#> dateSymbolChanged dateNameChanged dateModified ncbiGeneId ensemblGeneId
#> <Date> <Date> <Date> <integer> <character>
#> 5 NA NA 2023-01-20 1 ENSG00000121410
#> 7 NA NA 2023-01-20 2 ENSG00000175899
#> 8 2010-02-24 2010-02-24 2016-08-22 3 ENSG00000256069
#> 15 2013-08-22 2013-08-22 2014-11-18 11 ENSG00000253937
#> 16 NA 2016-04-06 2023-01-20 12 ENSG00000196136
#> ... ... ... ... ... ...
#> 56900 NA NA 2023-09-14 644051 ENSG00000234115
#> 56902 NA NA 2023-09-14 100421092 ENSG00000219314
#> 56903 NA NA 2023-09-14 132243159 ENSG00000219404
#> 56904 NA NA 2023-09-14 100128365 ENSG00000220748
#> 56905 NA NA 2023-09-14 100421976 ENSG00000255710
#> vegaId ucscId ena refseqAccession
#> <character> <character> <CharacterList> <CharacterList>
#> 5 OTTHUMG00000183507 uc002qsd.5 NA NM_130786
#> 7 OTTHUMG00000150267 uc001qvk.2 BX647329,X68728,M11313 NM_000014
#> 8 OTTHUMG00000168334 NA M24415 NG_001067
#> 15 OTTHUMG00000163710 NA X17060 NG_004857
#> 16 OTTHUMG00000029851 uc001yds.4 K01500 NM_001085
#> ... ... ... ... ...
#> 56900 NA NA NA NG_005686
#> 56902 NA NA NA NG_025901
#> 56903 NA NA NA NG_231581
#> 56904 NA NA NA NG_022347
#> 56905 NA NA NA NG_024420
#> ccdsId uniprotIds pubmedId
#> <CharacterList> <CharacterList> <CharacterList>
#> 5 CCDS12976 P04217 2591067
#> 7 CCDS44827 P01023 2408344,9697696
#> 8 NA NA 2478422
#> 15 NA NA 2340091,9284941
#> 16 CCDS32150 P01011 3260956,24172014
#> ... ... ... ...
#> 56900 NA NA NA
#> 56902 NA NA NA
#> 56903 NA NA NA
#> 56904 NA NA NA
#> 56905 NA NA NA
#> mgdId rgdId
#> <CharacterList> <CharacterList>
#> 5 MGI:2152878 RGD:69417
#> 7 MGI:2449119 RGD:2004
#> 8 NA NA
#> 15 NA NA
#> 16 MGI:102848,MGI:105045,MGI:105046,... RGD:3747
#> ... ... ...
#> 56900 NA NA
#> 56902 NA NA
#> 56903 NA NA
#> 56904 NA NA
#> 56905 NA NA
#> lsdb cosmic omimId mirbase
#> <CharacterList> <character> <CharacterList> <character>
#> 5 NA NA 138670 NA
#> 7 LRG_591,http://ftp.ebi.ac.uk.. NA 103950 NA
#> 8 NA NA NA NA
#> 15 NA NA NA NA
#> 16 NA NA 107280 NA
#> ... ... ... ... ...
#> 56900 NA NA NA NA
#> 56902 NA NA NA NA
#> 56903 NA NA NA NA
#> 56904 NA NA NA NA
#> 56905 NA NA NA NA
#> homeodb snornabase bioparadigmsSlc orphanet pseudogeneOrg
#> <integer> <character> <character> <integer> <character>
#> 5 NA NA NA NA NA
#> 7 NA NA NA NA NA
#> 8 NA NA NA NA PGOHUM00000291221
#> 15 NA NA NA NA PGOHUM00000260428
#> 16 NA NA NA 200946 NA
#> ... ... ... ... ... ...
#> 56900 NA NA NA NA NA
#> 56902 NA NA NA NA NA
#> 56903 NA NA NA NA NA
#> 56904 NA NA NA NA NA
#> 56905 NA NA NA NA NA
#> hordeId merops imgt iuphar kznfGeneCatalog
#> <character> <character> <character> <character> <logical>
#> 5 NA I43.950 NA NA NA
#> 7 NA I39.001 NA NA NA
#> 8 NA NA NA NA NA
#> 15 NA NA NA NA NA
#> 16 NA I04.002 NA NA NA
#> ... ... ... ... ... ...
#> 56900 NA NA NA NA NA
#> 56902 NA NA NA NA NA
#> 56903 NA NA NA NA NA
#> 56904 NA NA NA NA NA
#> 56905 NA NA NA NA NA
#> mamitTrnadb cd lncrnadb enzymeId
#> <integer> <character> <character> <CharacterList>
#> 5 NA NA NA NA
#> 7 NA NA NA NA
#> 8 NA NA NA NA
#> 15 NA NA NA NA
#> 16 NA NA NA NA
#> ... ... ... ... ...
#> 56900 NA NA NA NA
#> 56902 NA NA NA NA
#> 56903 NA NA NA NA
#> 56904 NA NA NA NA
#> 56905 NA NA NA NA
#> intermediateFilamentDb rnaCentralIds lncipedia gtrnadb
#> <logical> <logical> <character> <character>
#> 5 NA NA NA NA
#> 7 NA NA NA NA
#> 8 NA NA NA NA
#> 15 NA NA NA NA
#> 16 NA NA NA NA
#> ... ... ... ... ...
#> 56900 NA NA NA NA
#> 56902 NA NA NA NA
#> 56903 NA NA NA NA
#> 56904 NA NA NA NA
#> 56905 NA NA NA NA
#> maneSelect
#> <CharacterList>
#> 5 ENST00000263100.8,NM_130786.4
#> 7 ENST00000318602.12,NM_000014.6
#> 8 NA
#> 15 NA
#> 16 ENST00000393078.5,NM_001085.5
#> ... ...
#> 56900 NA
#> 56902 NA
#> 56903 NA
#> 56904 NA
#> 56905 NA