HOCOMOCO: A comprehensive collection of human transcription factor binding sites models
AuthorsKulakovskiy, Ivan V.
Medvedeva, Yulia A.
Kasianov, Artem S.
Vorontsov, Ilya E.
Bajic, Vladimir B.
Makeev, Vsevolod J.
KAUST DepartmentComputational Bioscience Research Center (CBRC)
MetadataShow full item record
AbstractTranscription factor (TF) binding site (TFBS) models are crucial for computational reconstruction of transcription regulatory networks. In existing repositories, a TF often has several models (also called binding profiles or motifs), obtained from different experimental data. Having a single TFBS model for a TF is more pragmatic for practical applications. We show that integration of TFBS data from various types of experiments into a single model typically results in the improved model quality probably due to partial correction of source specific technique bias. We present the Homo sapiens comprehensive model collection (HOCOMOCO, http://autosome.ru/HOCOMOCO/, http://cbrc.kaust.edu.sa/ hocomoco/) containing carefully hand-curated TFBS models constructed by integration of binding sequences obtained by both low- and high-throughput methods. To construct position weight matrices to represent these TFBS models, we used ChIPMunk software in four computational modes, including newly developed periodic positional prior mode associated with DNA helix pitch. We selected only one TFBS model per TF, unless there was a clear experimental evidence for two rather distinct TFBS models. We assigned a quality rating to each model. HOCOMOCO contains 426 systematically curated TFBS models for 401 human TFs, where 172 models are based on more than one data source. The Author(s) 2012.
CitationKulakovskiy IV, Medvedeva YA, Schaefer U, Kasianov AS, Vorontsov IE, et al. (2012) HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. Nucleic Acids Research 41: D195-D202. doi:10.1093/nar/gks1089.
PublisherOxford University Press (OUP)
JournalNucleic Acids Research
PubMed Central IDPMC3531053
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- HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models.
- Authors: Kulakovskiy IV, Vorontsov IE, Yevshin IS, Soboleva AV, Kasianov AS, Ashoor H, Ba-Alawi W, Bajic VB, Medvedeva YA, Kolpakov FA, Makeev VJ
- Issue date: 2016 Jan 4
- HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis.
- Authors: Kulakovskiy IV, Vorontsov IE, Yevshin IS, Sharipov RN, Fedorova AD, Rumynskiy EI, Medvedeva YA, Magana-Mora A, Bajic VB, Papatsenko DA, Kolpakov FA, Makeev VJ
- Issue date: 2018 Jan 4
- Transcription Factor Information System (TFIS): A Tool for Detection of Transcription Factor Binding Sites.
- Authors: Narad P, Kumar A, Chakraborty A, Patni P, Sengupta A, Wadhwa G, Upadhyaya KC
- Issue date: 2017 Sep
- A novel method for improved accuracy of transcription factor binding site prediction.
- Authors: Khamis AM, Motwalli O, Oliva R, Jankovic BR, Medvedeva YA, Ashoor H, Essack M, Gao X, Bajic VB
- Issue date: 2018 Jul 6
- From binding motifs in ChIP-Seq data to improved models of transcription factor binding sites.
- Authors: Kulakovskiy I, Levitsky V, Oshchepkov D, Bryzgalov L, Vorontsov I, Makeev V
- Issue date: 2013 Feb
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