gravatar for michael.j.apostolides

4 hours ago by

Hi all,

I'm sure many of you have seen the new publication EpiMap that has come out in Nature which gives unprecedented epigenomic annotations for many tissue types.

www.nature.com/articles/s41586-020-03145-z

I am particularly interested in enhancers, their locations (in BED format), and their gene links (they mention in the paper that each enhancer regulates 1.5 genes on average, and each gene is regulated by 13 enhancers on average).

I am trying to find this data, but cannot seem to figure out how/whether this data is accessible. I see at the following links that there are various "Enhancer" files in "hdf5" and "mtx"formats (Enhancer_H3K27ac_intersect_matrix.hdf5, Enhancer_H3K27ac_intersect_matrix.mtx.gz).

personal.broadinstitute.org/cboix/epimap/mark_matrices/

I tried loading them in R to no avail (using "rhdf5::H5Fopen" and "Matrix:readMM" functions, respectively).

What I really need is a flat file with these data. For example, a previous publication, EnhancerAtlas, allows flat-file download for these:

www.enhanceratlas.org/downloadv2.php

For the sample, "GM12878", I can get enhancer locations in the following BED file:

www.enhanceratlas.org/data/download/enhancer/hs/GM12878.bed

The "enhancer-gene interactions" for that same sample can be found here:

www.enhanceratlas.org/data/AllEPs/hs/GM12878_EP.txt

The new "EpiMap" paper seems to have more detailed enhancer-gene links than ever before, so it would be great to be able to access the data like I can for EnhancerAtlas.

Best,
Michael



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