HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis
AuthorsKulakovskiy, Ivan V.
Vorontsov, Ilya E.
Yevshin, Ivan S.
Sharipov, Ruslan N.
Fedorova, Alla D.
Rumynskiy, Eugene I.
Medvedeva, Yulia A.
Bajic, Vladimir B.
Papatsenko, Dmitry A.
Kolpakov, Fedor A.
Makeev, Vsevolod J.
KAUST DepartmentComputational Bioscience Research Center (CBRC)
Computer Science Program
Applied Mathematics and Computational Science Program
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
KAUST Grant NumberBAS/1/1606-01-01
Permanent link to this recordhttp://hdl.handle.net/10754/626157
MetadataShow full item record
AbstractWe present a major update of the HOCOMOCO collection that consists of patterns describing DNA binding specificities for human and mouse transcription factors. In this release, we profited from a nearly doubled volume of published in vivo experiments on transcription factor (TF) binding to expand the repertoire of binding models, replace low-quality models previously based on in vitro data only and cover more than a hundred TFs with previously unknown binding specificities. This was achieved by systematic motif discovery from more than five thousand ChIP-Seq experiments uniformly processed within the BioUML framework with several ChIP-Seq peak calling tools and aggregated in the GTRD database. HOCOMOCO v11 contains binding models for 453 mouse and 680 human transcription factors and includes 1302 mononucleotide and 576 dinucleotide position weight matrices, which describe primary binding preferences of each transcription factor and reliable alternative binding specificities. An interactive interface and bulk downloads are available on the web: http://hocomoco.autosome.ru and http://www.cbrc.kaust.edu.sa/hocomoco11. In this release, we complement HOCOMOCO by MoLoTool (Motif Location Toolbox, http://molotool.autosome.ru) that applies HOCOMOCO models for visualization of binding sites in short DNA sequences.
CitationKulakovskiy IV, Vorontsov IE, Yevshin IS, Sharipov RN, Fedorova AD, et al. (2017) HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis. Nucleic Acids Research. Available: http://dx.doi.org/10.1093/nar/gkx1106.
SponsorsThe project was primarily supported by Russian Science Foundation [17-74-10188 to I.V.K.]; A.M.M. and V.B.B. were supported by King Abdullah University of Science and Technology (KAUST) [baseline fund BAS/1/1606-01-01 of V.B.B.]; I.E.V. was personally supported by the Skoltech Systems Biology Fellowship. Funding for open access charge: Russian Science Foundation [17–74–10188 to I.V.K.].
PublisherOxford University Press (OUP)
JournalNucleic Acids Research
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