Accurate prediction of cell type-specific transcription factor binding.
Cell type-specific
ChIP-seq
DNase-seq
Machine learning
Transcription factors
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
10 01 2019
10 01 2019
Historique:
received:
25
07
2018
accepted:
18
12
2018
entrez:
12
1
2019
pubmed:
12
1
2019
medline:
9
3
2019
Statut:
epublish
Résumé
Prediction of cell type-specific, in vivo transcription factor binding sites is one of the central challenges in regulatory genomics. Here, we present our approach that earned a shared first rank in the "ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge" in 2017. In post-challenge analyses, we benchmark the influence of different feature sets and find that chromatin accessibility and binding motifs are sufficient to yield state-of-the-art performance. Finally, we provide 682 lists of predicted peaks for a total of 31 transcription factors in 22 primary cell types and tissues and a user-friendly version of our approach, Catchitt, for download.
Identifiants
pubmed: 30630522
doi: 10.1186/s13059-018-1614-y
pii: 10.1186/s13059-018-1614-y
pmc: PMC6327544
doi:
Substances chimiques
Transcription Factors
0
Types de publication
Comparative Study
Evaluation Study
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
9Références
Genome Biol. 2014;15(10):482
pubmed: 25287278
Nat Methods. 2009 Apr;6(4):283-9
pubmed: 19305407
PLoS One. 2014 Mar 20;9(3):e92209
pubmed: 24651729
Genome Res. 2012 Sep;22(9):1723-34
pubmed: 22955984
Bioinformatics. 2016 Aug 15;32(16):2419-26
pubmed: 27153645
Methods. 2019 Aug 15;166:40-47
pubmed: 30922998
PLoS Comput Biol. 2017 Feb 24;13(2):e1005403
pubmed: 28234893
J Cell Biochem. 2008 May 1;104(1):237-50
pubmed: 17990281
Nat Methods. 2013 Dec;10(12):1213-8
pubmed: 24097267
Genome Res. 2012 Sep;22(9):1760-74
pubmed: 22955987
Genome Res. 2011 Mar;21(3):447-55
pubmed: 21106904
Nucleic Acids Res. 2017 May 5;45(8):4315-4329
pubmed: 28334916
PLoS One. 2015 Sep 25;10(9):e0138030
pubmed: 26406244
Nat Commun. 2018 Apr 11;9(1):1402
pubmed: 29643364
Bioinformatics. 2015 Aug 1;31(15):2595-7
pubmed: 25810428
Genome Res. 2012 Sep;22(9):1798-812
pubmed: 22955990
BMC Bioinformatics. 2016 Jan 11;17 Suppl 1:4
pubmed: 26818008
PLoS Comput Biol. 2013;9(8):e1003118
pubmed: 23950696
Bioinformatics. 2010 Jun 15;26(12):i334-42
pubmed: 20529925
BMC Bioinformatics. 2010 Mar 22;11:149
pubmed: 20307305
Nucleic Acids Res. 2015 Oct 15;43(18):e119
pubmed: 26116565
Mol Biol (Mosk). 2016 May-Jun;50(3):496-503
pubmed: 27414788
Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4459-64
pubmed: 15753290
Genome Biol. 2009;10(11):R129
pubmed: 19919681
Pac Symp Biocomput. 2013;:80-91
pubmed: 23424114
Nucleic Acids Res. 2013 Nov;41(21):e197
pubmed: 24057214
Nucleic Acids Res. 2017 Jan 9;45(1):54-66
pubmed: 27899623
Cell. 2013 Oct 24;155(3):713-24
pubmed: 24243024
Nat Biotechnol. 2015 Apr;33(4):364-76
pubmed: 25690853
Nat Biotechnol. 2014 Feb;32(2):171-178
pubmed: 24441470
Nucleic Acids Res. 2016 Jan 4;44(D1):D116-25
pubmed: 26586801
Trends Biochem Sci. 1998 Mar;23(3):109-13
pubmed: 9581503
BMC Bioinformatics. 2011 Aug 04;12:323
pubmed: 21816040
Genome Res. 2012 Sep;22(9):1711-22
pubmed: 22955983
Nucleic Acids Res. 1978 Sep;5(9):3157-70
pubmed: 212715
Bioinformatics. 2014 Nov 15;30(22):3143-51
pubmed: 25086003
Bioinformatics. 2015 Sep 1;31(17):2852-9
pubmed: 25957350
BMC Bioinformatics. 2017 Jul 27;18(1):355
pubmed: 28750606
Nucleic Acids Res. 2013 Nov;41(21):e201
pubmed: 24071585
Cancer Res. 2006 Jul 15;66(14):6899-902
pubmed: 16849531
Genome Biol. 2003;5(1):201
pubmed: 14709165
Science. 2007 Jun 8;316(5830):1497-502
pubmed: 17540862
Genome Res. 2008 Nov;18(11):1763-77
pubmed: 18836037
PLoS One. 2015 Mar 04;10(3):e0118432
pubmed: 25738806
Nat Commun. 2015 Feb 03;2:6186
pubmed: 25645053
Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):505-19
pubmed: 6364039
J Mol Biol. 1987 Feb 20;193(4):723-50
pubmed: 3612791
Nat Methods. 2015 Mar;12(3):265-72, 7 p following 272
pubmed: 25240437