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HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models

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Ivan V. Kulakovskiy; Ilya E. Vorontsov; Ivan S. Yevshin; Anastasiia V. Soboleva; Artem S. Kasianov; Haitham Ashoor; Wail Ba-alawi; Vladimir B. Bajic; Yulia A. Medvedeva; Fedor A. Kolpakov; Vsevolod J. Makeev

Nucl. Acids Res. (04 January 2016) 44 (D1): D116-D125.

doi: 10.1093/nar/gkv1249

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.