Database for Enhancers with Coordinates

Question

[dk0319]

Can anyone recommend some good databases for extracting bed files with enhancer coordinates. I have used UCSC in the past, I was hoping to find some alternatives

Answer 1

[jared.andrews07]

dbSuper contains bed files for super enhancers as well as their constituent elements (normal enhancers) for a whole bunch of different tissues, cell types, and cell lines.

Answer 2

[Zhilong Jia]

EnhancerDB

EpiMap

Answer 3

[Pratik]

There is Ensembl's too.

Here is information on it: https://useast.ensembl.org/info/genome/funcgen/regulatory_build.html

You could find the previous annotations here through some clicking:

http://ftp.ensembl.org/pub/

If you want to use GRCh38:

You could download, gunzip, then do something like:

grep Enhancer homo_sapiens.GRCh38.Regulatory_Build.regulatory_features.20210107.gff | cut -f1,4,5 | awk -F "\t" '{ print "chr" $1,$2,$3 }'

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There is also https://screen.encodeproject.org/ which I think Ensembl uses to curate their regulatory build file above.

Answer 4

[Papyrus]

Also check EnhancerAtlas, apart from coordinates it provides predictions for enhancer-gene target interactions, which may be useful.