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. 2018 Jan 4;46(D1):D252-D259.
doi: 10.1093/nar/gkx1106.

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

Ivan V Kulakovskiy  1   2   3 , Ilya E Vorontsov  2 , Ivan S Yevshin  4 , Ruslan N Sharipov  4   5   6 , Alla D Fedorova  7 , Eugene I Rumynskiy  2   8 , Yulia A Medvedeva  2   8   9 , Arturo Magana-Mora  10   11 , Vladimir B Bajic  11 , Dmitry A Papatsenko  3 , Fedor A Kolpakov  4   5 , Vsevolod J Makeev  1   2   8
Affiliations

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

Ivan V Kulakovskiy et al. Nucleic Acids Res. .

Abstract

We 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.

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Figures

Figure 1.
Figure 1.
Number of TFs (Y-axis) with the best available model of a given quality (X-axis). The number of the most reliable A-quality models is more than doubled in HOCOMOCO v11 comparing to v10.
Figure 2.
Figure 2.
The number of TFs with the best-performing TFBS models (Y-axis) constructed from the peaks obtained with a particular peak caller (X-axis).
Figure 3.
Figure 3.
Examples of TFBS models included in HOCOMOCO v11: (A) SMAD2/3 models exhibit fuzzy patterns; (B) two variants of ANDR composite elements: the palindromic site and the double box ANDR-FOX; (C) the ‘genuine’ NANOG binding site along the putative OCT4-SOX2/NANOG composite element (for clarity the nucleotide pileups are shown unscaled); (D) SP1/2 (canonical SP-family GC-box) and SP7 binding models.
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