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BMC Res Notes. 2018 Oct 23;11(1):756. doi: 10.1186/s13104-018-3856-x.

Genome-wide map of human and mouse transcription factor binding sites aggregated from ChIP-Seq data.

Author information

1
Vavilov Institute of General Genetics, Russian Academy of Sciences, GSP-1, Gubkina 3, Moscow, Russia, 119991.
2
BIOSOFT.RU Ltd, Russkaya 41/1, Novosibirsk, Russia, 630058.
3
Institute of Computational Technologies, Siberian Branch of the Russian Academy of Sciences, Akad. Rzhanova 6, Novosibirsk, Russia, 630090.
4
Novosibirsk State University, Pirogova 2, Novosibirsk, Russia, 630090.
5
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, GSP-1, Vavilova 32, Moscow, Russia, 119991.
6
Moscow Institute of Physics and Technology (State University), 9 Institutskiy per, Dolgoprudny, Russia, 141700.
7
Vavilov Institute of General Genetics, Russian Academy of Sciences, GSP-1, Gubkina 3, Moscow, Russia, 119991. ivan.kulakovskiy@gmail.com.
8
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, GSP-1, Vavilova 32, Moscow, Russia, 119991. ivan.kulakovskiy@gmail.com.
9
Institute of Mathematical Problems of Biology RAS-the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Vitkevicha 1, Pushchino, Russia, 142290. ivan.kulakovskiy@gmail.com.

Abstract

OBJECTIVES:

Mammalian genomics studies, especially those focusing on transcriptional regulation, require information on genomic locations of regulatory regions, particularly, transcription factor (TF) binding sites. There are plenty of published ChIP-Seq data on in vivo binding of transcription factors in different cell types and conditions. However, handling of thousands of separate data sets is often impractical and it is desirable to have a single global map of genomic regions potentially bound by a particular TF in any of studied cell types and conditions.

DATA DESCRIPTION:

Here we report human and mouse cistromes, the maps of genomic regions that are routinely identified as TF binding sites, organized by TF. We provide cistromes for 349 mouse and 599 human TFs. Given a TF, its cistrome regions are supported by evidence from several ChIP-Seq experiments or several computational tools, and, as an optional filter, contain occurrences of sequence motifs recognized by the TF. Using the cistrome, we provide an annotation of TF binding sites in the vicinity of human and mouse transcription start sites. This information is useful for selecting potential gene targets of transcription factors and detecting co-regulated genes in differential gene expression data.

KEYWORDS:

ChIP-Seq; Cistrome; Human and mouse; Regulatory regions; Target genes; Transcription factor binding sites

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