databases > DOI:10.25504/FAIRsharing.c1bjep

ready HOmo sapiens transcription factor COmprehensive MOdel COllection (HOCOMOCO)


General Information
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 provides a set of dinucleotide position weight matrices based on ChIP-Seq data. All the models were produced by the ChIPMunk motif discovery tool. Models are manually curated with assigning model quality ratings based upon benchmark studies or inherited from HOCOMOCO v9. 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. Other sequences of TF binding DNA regions were collected from existing databases and other public data. An appropriate TFBS model was selected for each TF, with similar models selected for related TFs. All TFBS models and initial binding segments data used for motif discovery were mapped to UniPROT IDs. TF coding genes are linked with GeneCards entries. DNA binding domains are linked with TF class database.

How to cite this record HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection (HOCOMOCO); DOI:; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 19 2019 7:55 a.m.

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Record updated: Dec. 5, 2016, 6:07 a.m. by The FAIRsharing Team.

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HOCOMOCO: a comprehensive collection of human transcription factor binding sites models.

Kulakovskiy IV,Medvedeva YA,Schaefer U,Kasianov AS,Vorontsov IE,Bajic VB,Makeev VJ
Nucleic Acids Res 2012

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

Kulakovskiy IV,Vorontsov IE,Yevshin IS,Soboleva AV,Kasianov AS,Ashoor H,Ba-Alawi W,Bajic VB,Medvedeva YA,Kolpakov FA,Makeev VJ
Nucleic Acids Res 2015

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Deep and wide digging for binding motifs in ChIP-Seq data.

Kulakovskiy IV,Boeva VA,Favorov AV,Makeev VJ
Bioinformatics 2010

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From binding motifs in ChIP-Seq data to improved models of transcription factor binding sites.

Kulakovskiy I,Levitsky V,Oshchepkov D,Bryzgalov L,Vorontsov I,Makeev V
J Bioinform Comput Biol 2013

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Jaccard index based similarity measure to compare transcription factor binding site models.

Vorontsov IE,Kulakovskiy IV,Makeev VJ
Algorithms Mol Biol 2013

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Grant Number(s)

  • 07.514.11.4005 (Russian Ministry of Science and Education State)

  • 07.514.11.4006 (Russian Ministry of Science and Education State)

  • 11.G34.31.0008 (Russian Ministry of Science and Education State)

  • 14-04-01838 (Russian Fund for Basic Research)

  • 14-50-00060 (Russian Science Foundation)

  • 15-34-20423 (Russian Fund for Basic Research)