Fig. 4

Positive/negative RF contact delineation analysis. The ability of different HiC data analysis approaches to distinguish positive from negative (control) contacts is measured, for various data sets, using the area under the receiver operating characteristic curve (AUROC) for univariate predictors using as input the predicted IF values. a, d CTCF-mediated contacts identified by ChIA-PET [33]. b, e RNAPII-mediated contacts identified by ChIA-PET [33], c, f Inferred enhancer-promoter linkages based on DHS correlation [35]. To allow for the comparison with HiCPlus and HMRFBayes, only contacts occurring on chromosomes 9 to 22, X, and Y, and within a distance of 1 Mb, are analyzed. Top (a–c) and bottom (d–f) rows represent the performance of the classifiers applied to Hi-C data of size 60.8M (10% of input set) and 608M (100% of input set), respectively. Genome-wide results for HIFI are shown in Additional file 1: Figure S8. Similar results are observed for ChIA-PET RAD21 (Additional file 1: Figure S9)