ImmuneRegulation: a web-based tool for identifying human immune regulatory elements.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
02 07 2019
02 07 2019
Historique:
accepted:
09
05
2019
revised:
03
05
2019
received:
06
03
2019
pubmed:
23
5
2019
medline:
27
5
2020
entrez:
23
5
2019
Statut:
ppublish
Résumé
Humans vary considerably both in their baseline and activated immune phenotypes. We developed a user-friendly open-access web portal, ImmuneRegulation, that enables users to interactively explore immune regulatory elements that drive cell-type or cohort-specific gene expression levels. ImmuneRegulation currently provides the largest centrally integrated resource on human transcriptome regulation across whole blood and blood cell types, including (i) ∼43,000 genotyped individuals with associated gene expression data from ∼51,000 experiments, yielding genetic variant-gene expression associations on ∼220 million eQTLs; (ii) 14 million transcription factor (TF)-binding region hits extracted from 1945 ChIP-seq studies; and (iii) the latest GWAS catalog with 67,230 published variant-trait associations. Users can interactively explore associations between queried gene(s) and their regulators (cis-eQTLs, trans-eQTLs or TFs) across multiple cohorts and studies. These regulators may explain genotype-dependent gene expression variations and be critical in selecting the ideal cohorts or cell types for follow-up studies or in developing predictive models. Overall, ImmuneRegulation significantly lowers the barriers between complex immune regulation data and researchers who want rapid, intuitive and high-quality access to the effects of regulatory elements on gene expression in multiple studies to empower investigators in translating these rich data into biological insights and clinical applications, and is freely available at https://immuneregulation.mssm.edu.
Identifiants
pubmed: 31114925
pii: 5494773
doi: 10.1093/nar/gkz450
pmc: PMC6602512
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
W142-W150Subventions
Organisme : NIAID NIH HHS
ID : U19 AI089992
Pays : United States
Organisme : NCATS NIH HHS
ID : UL1 TR001863
Pays : United States
Informations de copyright
© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.
Références
Cell. 2018 Nov 29;175(6):1701-1715.e16
pubmed: 30449622
Sci Rep. 2018 Jan 15;8(1):739
pubmed: 29335477
Nat Neurosci. 2014 Oct;17(10):1418-1428
pubmed: 25174004
Vaccine. 2013 Jun 19;31(28):2911-2
pubmed: 23648045
Mol Syst Biol. 2018 Aug 27;14(8):e7862
pubmed: 30150281
Nature. 2012 Sep 6;489(7414):57-74
pubmed: 22955616
Nat Biotechnol. 2011 Jan;29(1):24-6
pubmed: 21221095
Am J Hum Genet. 2007 Sep;81(3):559-75
pubmed: 17701901
PLoS Biol. 2011 Apr;9(4):e1001046
pubmed: 21526222
Nat Genet. 2013 Oct;45(10):1238-1243
pubmed: 24013639
Nature. 2007 Jun 14;447(7146):799-816
pubmed: 17571346
Genome Res. 2010 Sep;20(9):1297-303
pubmed: 20644199
Genome Res. 2012 Sep;22(9):1813-31
pubmed: 22955991
BMC Infect Dis. 2018 Jun 22;18(1):282
pubmed: 29929468
Nat Genet. 2013 Jun;45(6):580-5
pubmed: 23715323
Vaccine. 2015 Sep 29;33(40):5271-81
pubmed: 26232539
Nat Genet. 2017 Jan;49(1):139-145
pubmed: 27918533
Bioinformatics. 2011 Mar 1;27(5):718-9
pubmed: 21208982
Cell. 2004 Jan 23;116(2):247-57
pubmed: 14744435
JCI Insight. 2017 Jul 6;2(13):
pubmed: 28679950
BMC Res Notes. 2014 Dec 11;7:901
pubmed: 25495213
Trends Genet. 2008 Aug;24(8):408-15
pubmed: 18597885
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Nucleic Acids Res. 2016 Jan 4;44(D1):D726-32
pubmed: 26527727
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Nucleic Acids Res. 2014 Jan;42(Database issue):D1001-6
pubmed: 24316577