Fig. 5.

Promoter–enhancer predictions are supported by ChIP-seq data, DNA accessibility, evolutionary conservation, and chromHMM “Strong Enhancer” loci. Shown are the average signal for ChIP-seq and additional genomic data, over predicted enhancer regions using PSYCHIC (FDR < 1e-2, blue), HiCCUPS (green), Fit-Hi-C (q value < 1e-10 for IMR90 and hES, q < 1e-4 for mCO, orange) or random interactions (yellow). Notably, PSYCHIC predictions are generally more enriched for all enhancer-related data, while HiCCUPS and Fit-Hi-C predictions are more enriched for CTCF and Insulator marks. No chromHMM data was found for mES