HOCOMOCO: A comprehensive collection of human transcription factor binding sites models

Ivan V. Kulakovskiy*, Yulia A. Medvedeva, Ulf Schaefer, Artem S. Kasianov, Ilya E. Vorontsov, Vladimir B. Bajic, Vsevolod J. Makeev

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

168 Citations (Scopus)

Abstract

Transcription 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.

Original languageEnglish
Pages (from-to)D195-D202
JournalNucleic Acids Research
Volume41
Issue numberD1
DOIs
Publication statusPublished - 1 Jan 2013
Externally publishedYes

Bibliographical note

Funding Information:
Dynasty Foundation Fellowship [to I.V.K.]; Russian Foundation for Basic Research [12-04-32082-mol_a to I.V.K.]; Presidium of the Russian Academy of Sciences Program in Cellular and Molecular Biology; Presidium of the Russian Academy of Sciences Fundamental Research Subprogram ‘Gene pools dynamics and conservation’; Russian Ministry of Science and Education State Contract [07.514.11.4005]; Russian Ministry of Science and Education State Contract [07.514.11.4006]; Russian Ministry of Science and Education grant [11.G34.31.0008]. Funding for open access charge: Presidium of the Russian Academy of Sciences program in Cellular and Molecular Biology.

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