GTRD: an integrated view of transcription regulation.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
08 01 2021
08 01 2021
Historique:
accepted:
03
11
2020
revised:
18
10
2020
received:
15
09
2020
pubmed:
25
11
2020
medline:
21
1
2021
entrez:
24
11
2020
Statut:
ppublish
Résumé
The Gene Transcription Regulation Database (GTRD; http://gtrd.biouml.org/) contains uniformly annotated and processed NGS data related to gene transcription regulation: ChIP-seq, ChIP-exo, DNase-seq, MNase-seq, ATAC-seq and RNA-seq. With the latest release, the database has reached a new level of data integration. All cell types (cell lines and tissues) presented in the GTRD were arranged into a dictionary and linked with different ontologies (BRENDA, Cell Ontology, Uberon, Cellosaurus and Experimental Factor Ontology) and with related experiments in specialized databases on transcription regulation (FANTOM5, ENCODE and GTEx). The updated version of the GTRD provides an integrated view of transcription regulation through a dedicated web interface with advanced browsing and search capabilities, an integrated genome browser, and table reports by cell types, transcription factors, and genes of interest.
Identifiants
pubmed: 33231677
pii: 5999890
doi: 10.1093/nar/gkaa1057
pmc: PMC7778956
doi:
Substances chimiques
Transcription Factors
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
D104-D111Informations de copyright
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.
Références
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D108-10
pubmed: 16381825
Nat Commun. 2021 May 12;12(1):2751
pubmed: 33980847
Nucleic Acids Res. 2019 Jan 8;47(D1):D145-D154
pubmed: 30380113
Cell Syst. 2015 Dec 23;1(6):417-425
pubmed: 26771021
Nucleic Acids Res. 2019 Jul 2;47(W1):W225-W233
pubmed: 31131402
Nucleic Acids Res. 2018 Jan 4;46(D1):D343-D347
pubmed: 29087517
Nucleic Acids Res. 2020 Jan 8;48(D1):D882-D889
pubmed: 31713622
Bioinformatics. 2010 Apr 15;26(8):1112-8
pubmed: 20200009
Nat Genet. 2010 Mar;42(3):255-9
pubmed: 20118932
Plant Cell Physiol. 2013 Feb;54(2):e1
pubmed: 23220694
PLoS One. 2019 Aug 29;14(8):e0221760
pubmed: 31465497
Cell. 2011 Dec 9;147(6):1408-19
pubmed: 22153082
Nature. 2014 Mar 27;507(7493):462-70
pubmed: 24670764
Nat Biotechnol. 2015 Apr;33(4):395-401
pubmed: 25751057
Nat Rev Genet. 2014 Jul;15(7):453-68
pubmed: 24913666
Nucleic Acids Res. 2012 Jan;40(Database issue):D54-6
pubmed: 22009675
Bioinformatics. 2010 Sep 1;26(17):2204-7
pubmed: 20639541
Bioinformatics. 2014 Apr 1;30(7):1003-5
pubmed: 24227676
Genome Res. 2012 Sep;22(9):1813-31
pubmed: 22955991
Nucleic Acids Res. 2017 Jan 4;45(D1):D61-D67
pubmed: 27924024
J Biomol Tech. 2018 Jul;29(2):25-38
pubmed: 29805321
Stat Appl Genet Mol Biol. 2009;8:Article29
pubmed: 19572828
Nucleic Acids Res. 2019 Jan 8;47(D1):D752-D758
pubmed: 30407557
Cell. 2014 Sep 11;158(6):1431-1443
pubmed: 25215497
Nucleic Acids Res. 2013 Jan;41(Database issue):D991-5
pubmed: 23193258
BMC Res Notes. 2018 Oct 23;11(1):756
pubmed: 30352610
Nucleic Acids Res. 2020 Jan 8;48(D1):D682-D688
pubmed: 31691826
Trends Genet. 2013 Jan;29(1):11-22
pubmed: 23102583
Nucleic Acids Res. 2019 Jan 8;47(D1):D100-D105
pubmed: 30445619
Nucleic Acids Res. 2018 Jul 2;46(W1):W215-W220
pubmed: 29846656
Nat Genet. 2013 Jun;45(6):580-5
pubmed: 23715323
Nucleic Acids Res. 2018 Jan 4;46(D1):D252-D259
pubmed: 29140464
Genome Biol. 2012 Jan 31;13(1):R5
pubmed: 22293552
J Biomed Semantics. 2016 Jul 04;7(1):44
pubmed: 27377652
Cell. 2007 May 18;129(4):823-37
pubmed: 17512414
Nat Methods. 2013 Dec;10(12):1213-8
pubmed: 24097267
Nucleic Acids Res. 2019 Jan 8;47(D1):D542-D549
pubmed: 30395242
Genome Res. 2002 Jun;12(6):996-1006
pubmed: 12045153
Nucleic Acids Res. 2016 Jul 27;44(13):6055-69
pubmed: 27288444
Nucleic Acids Res. 2020 Jan 8;48(D1):D93-D100
pubmed: 31598675