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Candidate enhancers and promoters based on histone modifications
Below are the candidate promoters and enhancers in 23 mouse tissue/cell types and 12 human ENCODE cell lines. These elements were used in the main mouse ENCODE paper. The enhancers were predicted based on three histone marks, H3K4me1, H3K4me3 and H3K27ac, using a random-forest based algorithm as described here. The promoter prediction is based on the enrichment of H3K4me3 (both p-value and fold enrichment). The detail for the promoter prediction can be found in here. The files are not bed files that denote the interval of the cis-regulatory element; instead, it records the midpoint of the peak. Each PI is free to +/- a padded region that captures the cis-regulatory element at his/her discretion.
Download gene expression profiles used in the mouse ENCODE main paper here: link