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

Ilya E Vorontsov,Fedor A Kolpakov,Vsevolod J Makeev,Ivan S Yevshin,Alla D Fedorova,Ivan V Kulakovskiy,Ruslan N Sharipov

doi:10.1186/s13104-018-3856-x

Abstract

ObjectivesMammalian 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 descriptionHere 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.

Highlights

There are thousands of experimental data sets related to in vivo binding of human and mouse transcription factors (TFs), with chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) as the gold standard method
For practical applications it is useful to have such constituent binding regions being separated into different reproducibility categories, and annotated with occurrences of transcription factor binding motifs, to highlight likely genuine binding sites of each particular TF
Data description Here we present the human and mouse cistromes [3], the genome-wide maps of regions bound by TFs, obtained through systematic analysis of ChIP-Seq data

Summary

Introduction

There are thousands of experimental data sets related to in vivo binding of human and mouse transcription factors (TFs), with chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) as the gold standard method. *Correspondence: ivan.kulakovskiy@gmail.com 1 Vavilov Institute of General Genetics, Russian Academy of Sciences, GSP‐1, Gubkina 3, Moscow, Russia 119991 Full list of author information is available at the end of the article Meta-clusters provided in GTRD are the genome segments bound by the studied TF across several data sets.

Objectives

Results

Conclusion