Exploring functionally annotated transcriptional consensus regulatory elements with CONREL.
Journal
Database : the journal of biological databases and curation
ISSN: 1758-0463
Titre abrégé: Database (Oxford)
Pays: England
ID NLM: 101517697
Informations de publication
Date de publication:
01 01 2020
01 01 2020
Historique:
received:
19
03
2020
revised:
03
07
2020
accepted:
06
08
2020
entrez:
13
11
2020
pubmed:
14
11
2020
medline:
29
10
2021
Statut:
ppublish
Résumé
Understanding the interaction between human genome regulatory elements and transcription factors is fundamental to elucidate the structure of gene regulatory networks. Here we present CONREL, a web application that allows for the exploration of functionally annotated transcriptional 'consensus' regulatory elements at different levels of abstraction. CONREL provides an extensive collection of consensus promoters, enhancers and active enhancers for 198 cell-lines across 38 tissue types, which are also combined to provide global consensuses. In addition, 1000 Genomes Project genotype data and the 'total binding affinity' of thousands of transcription factor binding motifs at genomic regulatory elements is fully combined and exploited to characterize and annotate functional properties of our collection. Comparison with other available resources highlights the strengths and advantages of CONREL. CONREL can be used to explore genomic loci, specific genes or genomic regions of interest across different cell lines and tissue types. The resource is freely available at https://bcglab.cibio.unitn.it/conrel.
Identifiants
pubmed: 33186463
pii: 5981331
doi: 10.1093/database/baaa071
pmc: PMC7805434
pii:
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
Informations de copyright
© The Author(s) 2020. Published by Oxford University Press.
Références
Database (Oxford). 2017 Jan 1;2017:
pubmed: 28605766
Bioinformatics. 2010 Jan 15;26(2):287-9
pubmed: 19900953
Database (Oxford). 2015 Sep 05;2015:
pubmed: 26342387
Bioinformatics. 2006 Jul 15;22(14):e141-9
pubmed: 16873464
Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21931-6
pubmed: 21106759
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D108-10
pubmed: 16381825
Bioinformatics. 2008 Jul 1;24(13):i165-71
pubmed: 18586710
PLoS One. 2015 Nov 24;10(11):e0143627
pubmed: 26599758
Nature. 2015 Feb 19;518(7539):317-30
pubmed: 25693563
Nature. 2012 Sep 6;489(7414):57-74
pubmed: 22955616
Nucleic Acids Res. 2019 Feb 28;47(4):e21
pubmed: 30517703
Nature. 2009 May 7;459(7243):108-12
pubmed: 19295514
Nucleic Acids Res. 2018 Jan 4;46(D1):D380-D386
pubmed: 29087512
Nature. 2000 Jan 6;403(6765):41-5
pubmed: 10638745
Genome Biol. 2015 Mar 24;16:56
pubmed: 25887522
Nucleic Acids Res. 2013 Jan;41(Database issue):D214-20
pubmed: 23180783
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Mol Biol Evol. 2011 Aug;28(8):2173-83
pubmed: 21335606
Nucleic Acids Res. 2018 Jan 4;46(D1):D1284
pubmed: 29161433
Bioinformatics. 2016 Dec 1;32(23):3543-3551
pubmed: 27515742
Nat Protoc. 2011 Nov 03;6(12):1860-9
pubmed: 22051799
Genome Res. 2006 Aug;16(8):962-72
pubmed: 16809671
Nucleic Acids Res. 2018 Jan 4;46(D1):D252-D259
pubmed: 29140464
Nature. 2011 Feb 10;470(7333):279-83
pubmed: 21160473
Hum Genet. 2017 Nov;136(11-12):1477-1487
pubmed: 29101457
Nucleic Acids Res. 2015 Feb 27;43(4):e27
pubmed: 25477382