Fig. 4: Fragment size and cross-linking determine loop detection.
From: Systematic evaluation of chromosome conformation capture assays
a, ‘Upset’ plot of loops detected in protocols using HFFc6 cells showing the total number of loops detected in the FA–DpnII, FA + DSG–DpnII and FA + DSG–MNase protocols on the right side (gray bars), and the number of loops detected in one, two or three of these protocols (shown in black bars). Loops found with one or multiple protocols are connected with black dots. b, Pileups of the loops shown in a. Numbers in each pileup represent signal enrichment at the loop compared with local background (Methods). c, Scatter plots for the strength of individual loops calculated in the same way as in b between protocol pairs in HFFc6 cells. The plots display two sets of looping interactions: the union sets (red squares) and the intersection sets (blue circles) from the three protocols. The color scale represents the density of loop interactions.
