ReMap Database

Overview

ReMap 2022 is an integrative database of transcription factor (TF), cofactor, and chromatin regulator binding sites derived from uniformly reprocessed ChIP-seq experiments. The 2022 release catalogs 165 million non-redundant peaks from 8,113 ChIP-seq datasets covering 1,210 TFs across human (hg38/hg19), mouse (mm10), Drosophila, and Arabidopsis genomes. All peaks are called with a consistent pipeline from public GEO/ArrayExpress experiments. Access is via the ReMap 2022 REST API at https://remap2022.univ-amu.fr/api/ and bulk BED file downloads; no authentication required.

When to Use

• Finding all TFs with ChIP-seq peaks overlapping a genomic region of interest (e.g., a GWAS SNP locus or candidate enhancer)
• Retrieving TF peaks near a gene's transcription start site to map its proximal regulatory landscape
• Listing all TFs available in ReMap for human or mouse with their peak and dataset counts
• Filtering ChIP-seq peaks by regulatory biotype annotation (promoter, enhancer, exon, intron, intergenic) for a TF in a specific cell line
• Downloading a BED file of all binding peaks for a TF across all cell types for offline analysis
• Identifying co-binding TFs at a locus by querying all overlapping peaks and grouping by TF name
• Use jaspar-database instead when you need PWM/PFM sequence models of TF binding specificity rather than ChIP-seq peak locations
• For ENCODE-specific regulatory tracks and accessibility data use encode-database; ReMap aggregates TF binding peaks from many sources including ENCODE

Prerequisites