Format

Send to

Choose Destination
Nucleic Acids Res. 2018 Jan 4;46(D1):D252-D259. doi: 10.1093/nar/gkx1106.

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis.

Author information

1
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, GSP-1, Vavilova 32, Moscow, Russia.
2
Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, GSP-1, Gubkina 3, Moscow, Russia.
3
Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia.
4
BIOSOFT.RU Ltd, 630058, Russkaya 41/1, Novosibirsk, Russia.
5
Institute of Computational Technologies, Siberian Branch of the Russian Academy of Sciences, 630090, Akad. Rzhanova 6, Novosibirsk, Russia.
6
Novosibirsk State University, 630090, Pirogova 2, Novosibirsk, Russia.
7
Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234, Leninskiye Gory 1-73, Moscow, Russia.
8
Moscow Institute of Physics and Technology (State University), 141700, 9 Institutskiy per, Dolgoprudny, Russia.
9
Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, 2 Leninsky Ave. 33, Moscow, Russia.
10
National Institute of Advanced Industrial Science and Technology (AIST), Com. Bio Big-Data Open Innovation Lab. (CBBD-OIL), AIST Tokyo Waterfront Main Bldg. #323, 2-3-26 Aomi, Tokyo 135-0064, Japan.
11
King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia.

Abstract

We present a major update of the HOCOMOCO collection that consists of patterns describing DNA binding specificities for human and mouse transcription factors. In this release, we profited from a nearly doubled volume of published in vivo experiments on transcription factor (TF) binding to expand the repertoire of binding models, replace low-quality models previously based on in vitro data only and cover more than a hundred TFs with previously unknown binding specificities. This was achieved by systematic motif discovery from more than five thousand ChIP-Seq experiments uniformly processed within the BioUML framework with several ChIP-Seq peak calling tools and aggregated in the GTRD database. HOCOMOCO v11 contains binding models for 453 mouse and 680 human transcription factors and includes 1302 mononucleotide and 576 dinucleotide position weight matrices, which describe primary binding preferences of each transcription factor and reliable alternative binding specificities. An interactive interface and bulk downloads are available on the web: http://hocomoco.autosome.ru and http://www.cbrc.kaust.edu.sa/hocomoco11. In this release, we complement HOCOMOCO by MoLoTool (Motif Location Toolbox, http://molotool.autosome.ru) that applies HOCOMOCO models for visualization of binding sites in short DNA sequences.

PMID:
29140464
PMCID:
PMC5753240
DOI:
10.1093/nar/gkx1106
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center