We then used the cutree method to select 5 sub-clusters in each tree, starting from the root. Enhancers in each set were then extended +−300 nt from their midpoints, and CpG islands and observed / expected CpG ratios were calculated. The resulting sub-clusters broke up enhancers into 201 and 247 ubiquitous enhancers (u-enhancers) defined by cell type and tissue facets, respectively, (these sets intersect by 106 enhancers) and non-ubiquitous enhancers. To summarize the features of u-enhancers in terms of expression width and variance, identified in a single plot, we used those enhancers falling into u-enhancer group from the tissue clustering. We then plotted the mean TPM over all tissue facets, as well as the coefficient of variation (expression variance over all tissue facets scaled by mean expression). Then we repeated this for the remaining enhancers (non-u-enhancers).
