In order to visualize the complexity and specialization of facets according to usage and specificity score of enhancers and genes, we counted the frequency of facet-used enhancers (significantly expressed in at least one contained sample) and gene promoters (≥ 1 TPM in at least one sample) with a specificity score in any of 20 bins distributed between 0 and 1. The number of robustly expressed enhancers and genes per sample were normalized to enhancers and genes per million mapped tags, utilizing the total number of mapped CAGE tags in each sample, and further log-transformed. The counts per million mapped tags were visualized in box plots split by facet (only facets with more than one contained sample were considered).
