New public hub: VRMOD CRM

[Gerardo Perez]

Hello Everyone,

We are happy to announce the release of a new Public Hub, the VRMOD CRM track hub for hg38 and mm10. The Vertebrate Regulatory MOdule Detector (VRMOD) is a method that accurately predicts gene expression regulatory sequences using only the query genomic sequences. VRMOD was applied to 309 genomes from the Ensembl database, generating a compendium of high-resolution, genome-position-fixed cis-regulatory modules without adjusting any parameters.

This track hub displays experimentally defined, predicted, and epigenomically supported cis-regulatory elements across a wide range of tissues and cell types. The hub includes the following tracks:

• VRMOD CRM: Cis-regulatory modules (CRMs) predicted by the VRMOD algorithm.
• ExpCRMs: Literature-curated, experimentally defined human (n = 60) cis-regulatory modules driving gene expression in diverse tissues, cell types, and developmental stages.
• VISTA Enhancers: In vivo validated functional human enhancer elements (n = 998) obtained from the VISTA Enhancer Browser.
• ENCODE_V2: Human candidate cis-regulatory elements (cCREs) obtained from ENCODE V2.
• ENCODE_V3: Human candidate cis-regulatory elements (cCREs) obtained from ENCODE V3.
• ENCODE_V4: Human candidate cis-regulatory elements (cCREs) obtained from ENCODE V4.
• Cistrome ATAC: Human ATAC-seq peaks from the Cistrome database derived from 1,059 samples across 25 tissue and cell types.
• Cistrome DHS: DNase I hypersensitive site (DHS) peaks from human DNase-seq data obtained from the Cistrome database.
• Cistrome H3K27ac: Human ChIP-seq peaks for the histone mark H3K27ac downloaded from the Cistrome database.
• Cistrome H3K4me1: Human ChIP-seq peaks for the histone mark H3K4me1 downloaded from the Cistrome database.
• Cistrome H3K4me3: Human ChIP-seq peaks for the histone mark H3K4me3 downloaded from the Cistrome database.
• Enhancer Atlas: Putative human enhancers obtained from Enhancer Atlas 2.0.
• scATAC-seq: Human scATAC-seq peaks derived from 45 adult and fetal tissues and 222 cell types.
• QTL_SNPs: Significant neurodegenerative disease–associated eQTL SNPs compiled from ten published datasets.

We would like to thank the Zhao Lab at Washington University School of Medicine for creating this hub, as well as the teams behind Cistrome, Enhancer Atlas, VISTA, ENCODE, and related resources.