ReMap

ReMap provides comprehensive, manually curated catalogs of regulatory regions by integrating large-scale DNA-binding experiments (ChIP-seq, ChIP-exo, DAP-seq) across Homo sapiens, Mus musculus, Drosophila melanogaster, and Arabidopsis thaliana.

Key Features:

• Extensive Data Integration: Processed over 11,000 DNA-binding sequencing datasets across four species, with reported human atlases described as 5,798 datasets/1,135 transcriptional regulators/165 million peaks and alternatively 8,103 datasets/1,210 transcriptional regulators/182 million peaks.
• Species-Specific Catalogs: Human: 8,103 datasets, 182 million peaks, 1,210 TRs; Mouse: 5,503 ChIP-seq datasets, 123 million peaks, 648 TRs; Drosophila melanogaster: 1,205 datasets, 16.6 million peaks, 550 TRs; Arabidopsis thaliana: a catalog with 372 TRs and 2.6 million peaks and a histone modification catalog of 33 marks totaling 4.5 million peaks.
• Data Sources and Assays: Integrates datasets from GEO, ENCODE, and ENA and processes ChIP-seq, ChIP-exo, and DAP-seq experiments.
• Enhanced Regulatory Search Space: Integration with public ChIP-seq datasets and ENCODE TF maps increased the human genome regulatory search space by 14% relative to ENCODE alone.
• Cis Regulatory Module Identification: Includes a reported novel method for identifying Cis Regulatory Modules.

Scientific Applications:

• Genome-wide regulatory element annotation: Generation of comprehensive catalogs supports identification and annotation of regulatory regions across four model organisms.
• Transcription factor and chromatin studies: Enables analysis of transcriptional regulator binding repertoires and chromatin modifications using integrated ChIP-seq, ChIP-exo, and DAP-seq data.
• Cancer regulatory variant annotation: Has been applied to annotate variant enhancer loci (VELs) from H3K4me1 marks in cancer cell lines to investigate non-coding regions involved in cancer development and proliferation.

Methodology:

Integrates and processes ChIP-seq, ChIP-exo, and DAP-seq datasets from GEO, ENCODE, and ENA; performs manual curation of resulting catalogs; integrates public ChIP-seq datasets with ENCODE TF maps; implements a method for identifying Cis Regulatory Modules.