Figure 2.

Promoter and Promoter Flank Accessibility Is Highly Predictable, but Enhancers Show Variability

(A) Promoter flank (pf) accessibility is highly predictable (PR AUC = 0.839), as shown by the genomic site performance breakdown over all samples in the held-out tissues test set. The orange line indicates overall PR AUC computed across all test samples and all sites.

(B) No clear performance difference was observed when genomic sites across the held-out tissue test set were split into those that did (in L1000) and did not (non-L1000) overlap the L1000 RNA-seq input gene set. Note that not all sites overlapped with known gene regions, so the union of the L1000 and non-L1000 subsets did not always make up the complete set of sites of a certain type.

(C) Overall metrics separated by tissue type show that some held-out tissues in the test set were more challenging as reflected by lower AUCs.

(D) Predictions at enhancers were highly variable between samples, even with good PR AUC, and performance on pf regions remained consistently high, even for tissues where overall results were lowest.