Fig. 2

Examples of interactions called by CHiCAGO. Top panels: plots showing the read counts from bait-other end pairs within 500 kb (upstream and downstream) of two baits, containing the promoters of a VEZF1 and b RGS22 in GM12878 cells. Significant interactions detected by CHiCAGO (score ≥5) are shown in red, and sub-threshold interactions (3 ≤ score < 5) are shown in blue. Triangles indicate bait-to-bait interactions. Grey lines show expected counts and dashed lines the upper bound of the 95 % confidence intervals. (Note that bait-to-bait interactions have higher expected read counts than bait-to-non-bait interactions spanning the same distance.) Bottom panels: the genomic maps of the corresponding regions, with coloured bars showing “chromatin colours” obtained from performing chromatin segmentation with chromHMM [60]: red, active promoter; pink, poised/repressed promoter; orange, strong enhancer; yellow, weak enhancer; blue, insulator