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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) v10 provides transcription factor (TF) binding models for 601 human and 396 mouse TFs.

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

All the models were produced by the ChIPMunk motif discovery tool.Model quality ratings are based on a comprehensive benchmark study or inherited from HOCOMOCO v9.

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