Fig. 2

Regions exhibited higher cross-correlation with their matching shapes than with randomly learned shapes. The density plots indicate the distribution of cross-correlations between regions and their matching shapes for all regions, and the color denotes the RE annotation (red—weak, blue—enhancer, green—promoter). Statistically higher cross-correlations were found between shapes learned using the original, unpermuted signal and their matching regions than between shapes learned using permuted signal and their matching regions. In all samples, the permuted shapes were associated with only weak or unknown REs