VDJbase: an adaptive immune receptor genotype and haplotype database.
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 2020
08 01 2020
Historique:
accepted:
01
10
2019
revised:
19
09
2019
received:
11
08
2019
pubmed:
12
10
2019
medline:
19
5
2020
entrez:
12
10
2019
Statut:
ppublish
Résumé
VDJbase is a publicly available database that offers easy searching of data describing the complete sets of gene sequences (genotypes and haplotypes) inferred from adaptive immune receptor repertoire sequencing datasets. VDJbase is designed to act as a resource that will allow the scientific community to explore the genetic variability of the immunoglobulin (Ig) and T cell receptor (TR) gene loci. It can also assist in the investigation of Ig- and TR-related genetic predispositions to diseases. Our database includes web-based query and online tools to assist in visualization and analysis of the genotype and haplotype data. It enables users to detect those alleles and genes that are significantly over-represented in a particular population, in terms of genotype, haplotype and gene expression. The database website can be freely accessed at https://www.vdjbase.org/, and no login is required. The data and code use creative common licenses and are freely downloadable from https://bitbucket.org/account/user/yaarilab/projects/GPHP.
Identifiants
pubmed: 31602484
pii: 5585549
doi: 10.1093/nar/gkz872
pmc: PMC6943044
doi:
Substances chimiques
Receptors, Antigen, B-Cell
0
Receptors, Antigen, T-Cell
0
Receptors, Immunologic
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
D1051-D1056Subventions
Organisme : NIAID NIH HHS
ID : R01 AI127877
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI125567
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI130398
Pays : United States
Informations de copyright
© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.
Références
J Allergy Clin Immunol. 2016 Jan;137(1):157-167
pubmed: 26152318
Cell Rep. 2016 Nov 1;17(6):1560-1570
pubmed: 27806295
Philos Trans R Soc Lond B Biol Sci. 2015 Sep 5;370(1676):null
pubmed: 26194751
Am J Hum Genet. 2013 Apr 4;92(4):530-46
pubmed: 23541343
Bioinformatics. 2015 Oct 15;31(20):3356-8
pubmed: 26069265
Bioinformatics. 2018 Jul 1;34(13):i341-i349
pubmed: 29949968
Nat Biotechnol. 2014 Feb;32(2):158-68
pubmed: 24441474
Nat Biotechnol. 2012 May 07;30(5):423-33
pubmed: 22565972
Integr Biol (Camb). 2015 Dec;7(12):1587-97
pubmed: 26481611
Nucleic Acids Res. 2009 Jan;37(Database issue):D1006-12
pubmed: 18978023
J Immunol. 2015 May 1;194(9):4371-8
pubmed: 25825450
Nat Rev Rheumatol. 2015 Mar;11(3):171-82
pubmed: 25536486
Trends Immunol. 2017 Jul;38(7):459-470
pubmed: 28539189
Immunogenetics. 2012 Jan;64(1):3-14
pubmed: 21789596
J Immunol. 2017 May 1;198(9):3371-3373
pubmed: 28416712
PLoS Comput Biol. 2016 Jan 11;12(1):e1004409
pubmed: 26751373
Mol Immunol. 2017 Jul;87:12-22
pubmed: 28388445
J Immunol. 2015 Jun 15;194(12):5703-12
pubmed: 25972486
Immunol Rev. 2017 Jan;275(1):145-160
pubmed: 28133802
Genome Med. 2015 Nov 20;7:121
pubmed: 26589402
Immunol Cell Biol. 2008 Feb;86(2):111-5
pubmed: 18040280
Front Immunol. 2019 Mar 18;10:435
pubmed: 30936866
J Immunol. 2012 Feb 1;188(3):1333-40
pubmed: 22205028
Front Immunol. 2017 Nov 01;8:1418
pubmed: 29163494
Bioinformatics. 2019 Nov 1;35(22):4840-4842
pubmed: 31173062
Front Immunol. 2013 Nov 15;4:358
pubmed: 24298272
J Immunol. 2017 Feb 15;198(4):1460-1473
pubmed: 28087666
Front Immunol. 2019 Feb 13;10:129
pubmed: 30814994
Nat Commun. 2016 Dec 20;7:13642
pubmed: 27995928
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W34-40
pubmed: 23671333
Sci Transl Med. 2014 Aug 6;6(248):248ra107
pubmed: 25100741
Sci Rep. 2016 Feb 16;6:20842
pubmed: 26880249
Nat Commun. 2019 Feb 7;10(1):628
pubmed: 30733445
Proc Natl Acad Sci U S A. 2015 Feb 24;112(8):E862-70
pubmed: 25675496
Sci Transl Med. 2019 Feb 27;11(481):
pubmed: 30814336