ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments

By Jeanne Chèneby, Marius Gheorghe, Marie Artufel, Anthony Mathelier, B. Ballester. 2017

207 citations recorded by the source corpus.

Abstract With this latest release of ReMap (http://remap.cisreg.eu), we present a unique collection of regulatory regions in human, as a result of a large-scale integrative analysis of ChIP-seq experiments for hundreds of transcriptional regulators (TRs) such as transcription factors, transcriptional co-activators and chromatin regulators. In 2015, we introduced the ReMap database to capture the genome regulatory space by integrating public ChIP-seq datasets, covering 237 TRs across 13 million (M) peaks. In this release, we have extended this catalog to constitute a unique collection of regulatory regions. Specifically, we have collected, analyzed and retained after quality control a total of 2829 ChIP-seq datasets available from public sources, covering a total of 485 TRs with a catalog of 80M peaks. Additionally, the updated database includes new search features for TR names as well as aliases, including cell line names and the ability to navigate the data directly within genome browsers via public track hubs. Finally, full access to this catalog is available online together with a TR binding enrichment analysis tool. ReMap 2018 provides a significant update of the ReMap database, providing an in depth view of the complexity of the regulatory landscape in human.

Subfields: Molecular Biology

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Citations in the corpus

CADD: predicting the deleteriousness of variants throughout the human genome (2018, methodology): “Gene annotations: same processing as for GRCh37 via VEP Grantham: not specific to genome build phastCons, phyloP, GERP++: novel score generated based on multiz100way alignment of hg38 from UCSC genome browser (excluding the human genome sequence in calculation) bstatistic (11): liftover from hg18 mi”
Benchmark and integration of resources for the estimation of human transcription factor activities (2018, methodology): “ChIP-seq interactions We downloaded the merged ChIP-seq binding peaks provided by ReMap48 from ENCODE and other public resources.”
PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants (2018, background): “For example, ReMap currently increased their ChIP-seq collection and provided an exhaustive review of regulatory maps (5).”
Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis (2018, background): “Although there are other ChIP-seq databases, including ChIP-Atlas (BioRxiv: https://doi.org/10.1101/262899), ChIPBase (20) and ReMap (21), the Cistrome DB differs from these in terms of sample coverage, comprehensive quality control metrics, data browsing and querying capabilities, and downstream an”
hTFtarget: A Comprehensive Database for Regulations of Human Transcription Factors and Their Targets (2019, unknown): “The ReMap database just provides peak information for TFs in ChIP-Seq datasets.”
The UCSC Genome Browser database: 2019 update (2018, background): “Examples include cis-regulatory annotations created by JASPAR (3), ReMap (4), the Eukaryotic Promoter Database (5), ENCODE(6), the Ensembl regulatory build (7) and Brain and Roadmap Epigenomics (8), RNAs from FANTOM5 (9), Mouse Alleles from MGI (10), lncRNAs from LNCipedia (11), Cancer genomics (sho”
JASPAR 2020: update of the open-access database of transcription factor binding profiles (2019, methodology): “The new PFMs were derived from HT-SELEX (30), PBMs (20), ChIP-seq and DAP-seq experiments (data sourced from CistromeDB (31), ReMap (32,33), GTRD (34), ChIP-atlas (35) and ModERN (36), see Supplementary Text for method details).”