Prediction of enhancer-gene links for each Roadmap Epigenomics reference epigenome
is available in this zip file (212MB).
Files in the zipfile have the naming links_EPIGENOMEID_ENHANCERSTATE_2.5.txt.
EPIGENOMEID corresponds to the ID of the Reference Epigenome. Meta-data for the reference epigenome
here. ENHANCERSTATENUMOF15STATEOBSERVEDMODEL corresponds to the state number of one of the candidate enhancer chromatin states from the 15-state observed
model from (Roadmap Epigenomics Consortium et al, 2015). Predictions have been made separately for states 6_EnhG, 7_Enh, and 12_EnhBiv and for each reference
epigenome. The files are six-column tab delimited with the columns as follows:
(2) start coordinate of 200-bp bin (0-based inclusive)
(3) end coordinate of 200-bp bin (0-based exclusive)
(4) ensembl gene ID
(5) prediction confidence score
(6) position relative to TSS
Predictions are made separately for each 200bp bin.
Only enhancer-gene links with a confidence score greater than or equal to 2.5 are included in the file.
The general approach to generate these links was described in (Ernst et al, 2011) with
specific changes described in (Liu et al, 2017).
The data used to generate these links was described in (Roadmap Epigenomics Consortium et al, 2015).
Code used to generate the links can be found here,
which also uses the Weka software.