Comprehensive Enhancer Identification via Multi-Omics

The consensus enhancers in EnhancerAtlas 2.0 were identified based on twelve high-throughput experimental approaches, including P300 (12 (link)), Histone (10 (link)), POLR2A (13 (link),21 (link)), TF-binding (11 (link)), DHS (or ATAC) (8 (link),9 (link)), FAIRE (16 (link)), MNase-seq (14 (link),15 (link)), GRO-seq (6 (link)), STARR-seq (5 (link)), CAGE (2 (link)), ChIA-PET (20 (link)) and MPRA (17 (link)). We manually downloaded 16 055 datasets, including processed or the raw sequencing data, from NCBI GEO datasets (36 (link)), ENCODE project portal at UCSC (32 (link)), Epigenome Roadmap (7 (link)) and FANTOM5 (2 (link)). The datasets in Homo sapiens, Sus scrofa, Rattus norvegicus, Mus musculus, Gallus gallus, Danio rerio, Drosophila melanogaster, Caenorhabditis elegans and Saccharomyces cerevisiae were mapped to hg19, susScr3, rn5, mm9, galGal4, danRer10, dm3, ce10 and sacCer3, respectively.

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Gao T, & Qian J. (2019). EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species. Nucleic Acids Research, 48(D1), D58-D64.

Publication 2019

Atac Caenorhabditis elegans Chia pet Danio rerio Drosophila melanogaster Epigenome Gallus gallus Histone Homo sapiens Mus musculus P300 Rattus norvegicus Saccharomyces cerevisiae Sus scrofa

Corresponding Organization : Sidney Kimmel Comprehensive Cancer Center

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Protocol cited in 31 other protocols

Variable analysis

independent variables

Histone
POLR2A
TF-binding
DHS (or ATAC)
FAIRE
MNase-seq
GRO-seq
STARR-seq
ChIA-PET

dependent variables

Consensus enhancers in EnhancerAtlas 2.0

control variables

Datasets in Homo sapiens, Sus scrofa, Rattus norvegicus, Mus musculus, Gallus gallus, Danio rerio, Drosophila melanogaster, Caenorhabditis elegans and Saccharomyces cerevisiae were mapped to hg19, susScr3, rn5, mm9, galGal4, danRer10, dm3, ce10 and sacCer3, respectively.

Annotations

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