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

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Ivan V. Kulakovskiy; Ilya E. Vorontsov; Ivan S. Yevshin; Ruslan N. Sharipov; Alla D. Fedorova; Eugene I. Rumynskiy; Yulia A. Medvedeva; Arturo Magana-Mora; Vladimir B. Bajic; Dmitry A. Papatsenko; Fedor A. Kolpakov; Vsevolod J. Makeev

Nucl. Acids Res., Database issue, gkx1106 (11 November 2017)

doi: 10.1093/nar/gkx1106

HOmo sapiens COmprehensive MOdel COllection (HOCOMOCO) v11 provides transcription factor (TF) binding models for 680 human and 453 mouse TFs.

Since v11, HOCOMOCO is complemented by MoLoTool, an interactive web tool to mark motif occurrences in a given set of DNA sequences.

In addition to basic mononucleotide position weight matrices (PWMs), HOCOMOCO provides dinucleotide position weight matrices based on ChIP-Seq data.

All the models were produced by the ChIPMunk motif discovery tool. Model quality ratings are results of a comprehensive cross-validation benchmark.

ChIP-Seq data for motif discovery was extracted from GTRD database of BioUML platform, that also provides an interface for motif finding (sequence scanning) with HOCOMOCO models.