Fig. 5

Comparison with Hi-C. (a) Correlation between the median pairwise distances and the corresponding contact frequencies determined by Hi-C for all the 16 miFISH probes (Dataset 1²³). n, number of probe pairs. (b) Correlation between the contact frequencies between each pair of 16 miFISH probes (whereby dots located 1 μm or less apart are considered as being in contact) and the corresponding contact frequencies measured by Hi-C. (c) Same as in (a) but using less stringent dot assignment criteria by allowing the possibility that dots are assigned to multiple dual-color probes. (d) Same as in (a) but using a more relaxed threshold (0.55 µm) for the overlap between two dots. (e) Same as in (a) but using a different pipeline that allocates dots in a random manner to a probe. In all the plots in the figure, the dashed lines represent linear regression. PCC, Pearson’s correlation coefficient. SCC, Spearman’s correlation coefficient. Each dot is colored based on the normalized distance from the lamina (see Methods for how the normalization was done). In all the scatter plots in the figure, each dot represents one of 120 possible probe pairs using the 16 miFISH probes.