Fig. 4: Comparison of three-way contacts predicted by DIMES with imaging experimental data.

a (Left) Pearson correlation coefficient, \(\rho ({\pi }_{ijk}^{\exp },{\pi }_{ijk}^{{{{{{{{\rm{model}}}}}}}}})\) versus a, where a is the threshold distance for contact formation. \({\pi }_{ijk}^{\exp }\) (\({\pi }_{ijk}^{{{{{{{{\rm{DIMES}}}}}}}}}\)) are the probabilities of co-localization of three loci (i, j, k), defined as π_ijk = Pr(r_ij < a, r_jk < a, r_ik < a). (Right) Plot of \({\pi }_{ijk}^{{{{{{{{\rm{DIMES}}}}}}}}}\) versus \({\pi }_{ijk}^{\exp }\) for a = 300 nm at which the \(\rho ({\pi }_{ijk}^{\exp },{\pi }_{ijk}^{{{{{{{{\rm{DIMES}}}}}}}}})\) is a maximum. b Comparison between the heatmaps for \({\pi }_{ijk}^{\exp }\) (lower triangle) and \({\pi }_{ijk}^{{{{{{{{\rm{DIMES}}}}}}}}}\) (upper triangle) for i = 11. The scale on the right gives π_11,j,k. c Same as (b) except it compares \({Z}_{ijk}^{\exp }\) (lower triangle) \({Z}_{ijk}^{{{{{{{{\rm{DIMES}}}}}}}}}\). Z_ijk = (π_ijk − μ(π_ijk))/σ(π_ijk) where μ(π_ijk) = ∑_m,n,qδ(∣j − i∣∣k − j∣ − ∣m − n∣∣n − q∣)π_mnq/∑_m,n,qδ(∣j − i∣∣k − j∣ − ∣m − n∣∣n − q∣), and σ(π_ijk) is the standard deviation. The Z_11,j,k scale is on the right. d Scatter plot of \({Z}_{ijk}^{{{{{{{{\rm{DIMES}}}}}}}}}\) versus \({Z}_{ijk}^{\exp }\) for i = 11. e Three individual chromosome conformations with the constraint that loci (1, 11, 31) be colocalized (a = 300 nm). f (Top) Mean distance map for cell-line IMR90 with 10 triplet sets (orange circles) with 10 largest Z_ijk values. (Middle) Same as the orange circles in the top panel, but plotted horizontally for easier comparison with the bottom panel. (Bottom) The CTCF Peak track plotted using Chip-seq data⁶⁹.