Fig. 3

Evaluation of unsupervised methods for predicting cCRE-gene pairs. a Precision-recall (PR) curves for four unsupervised methods evaluated on RNAPII ChIA-PET pairs in GM12878: distance between cCREs-ELS and genes (gray), DNase-DNase correlation by Thurman et al. (green), DNase-expression correlation by Sheffield et al. (purple), and the average rank of the distance and the DNase-expression method (black). The areas under the PR curve (AUPRs) for the four methods are listed in the legend. The AUPR for a random method is indicated with a dashed line at 0.15. b The AUPRs for the four unsupervised methods are computed for each of the six benchmark datasets from LCLs. c Genome browser view (chr6:88,382,922-88,515,031) of epigenomic signals and positive BENGI links (RNAPII ChIA-PET in red, Hi-C in green, CHi-C in blue, and GEUVADIS eQTL in pink) connecting the EH37E0853090 cCRE (star) to the AKIRIN2 gene. d Scatter plot of normalized AKIRIN2 expression vs. the normalized DNase signal at EH37E0853090 as calculated by Sheffield et al. (Pearson correlation coefficient = 0.16). Although AKIRIN2 is highly expressed across many tissues, EH37E0853090 presents high DNase signals primarily in lymphoblastoid cell lines (purple triangles), resulting in a low correlation