ReMap 2018, an atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments. LiftOver from hg38.
Description
Collection of regulatory regions in human deriving from 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.
The ReMap 2018 collection comprises a total of 2829 ChIP-seq datasets covering a total of 485 TRs with a catalog of 80M peaks.
the treatment being optional.
In general, transcription factors are identified by the HGNC gene symbol of
the targeted protein. Most of the original ChIP-seq target names were retained,
with the following exceptions:
CREBBP-R742me2a, CREBBP-R768me2a: post-translational modification (methylation)
at R residues in CREBBP. me2a means asymmetric dimethylarginine.
ESR1-S118P: phosphorylated serine 118 of ESR1 protein.
KDM1A-Isf+8a: LSD1+8a isoform of KDM1A.
MBD1-Isf1: MBD1 isoform 1.
PGR-IsfA, PGR-IsfB: two isoforms of PGR due to two different promoters.
RBP2_IsfL: large (L) RBP2 isoform.
TBXT: T-box transcription factor T (previous: T brachyury transcription factor).
TP53-S15P: phosphorylated serine 15 (S15P) of TP53.
TP53_PS46: phosphorylated serine 46 (S46P) of TP53.
TP73-DeltaN: isoform with N-terminal deletion (DeltaN).
TP73-TA: trans-activation (TA) domain.
Technical Notes
Data files were first lifted over from hg38, and converted to SGA using bed2sga
(ChIP-Seq v. 1.5.4).
References
Chèneby J, Gheorghe M, Artufel M, Mathelier A, BallesterB ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments.
Nucleic Acids Res. 2018 Jan 4;46(D1):D267-D275. doi: 10.1093/nar/gkx1092.
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