Extended Data Fig. 7: Intrinsic properties of method-specific contact subsets and contacts common between GAM and Hi-C.

a, Distribution by genomic distance of GAM-specific (red) and Hi-C-specific (blue) contacts. b, Upset plot presenting the agreement between sets of differential contacts obtained by different data transformations (Z-score transformation; Observed over expected, O/E; Rank transformation). The fraction of contacts in the intersections designated as GAM-specific or Hi-C-specific is colored in red and blue, respectively. c, Decile distributions of contact intensities before and after z-score transformation for the sets of GAM-specific contacts, Hi-C-specific contacts, and Strong-and-common contacts. d, Detectability of GAM-specific contacts, Hi-C-specific contacts, and Strong-and-common contacts. Windows are split into decile groups based on their detectability. Heatmaps show the log-scaled number of contacts connecting windows in different detectability deciles. Top: Deciles calculated by Hi-C detectability (total number of ligation events per window). Bottom: Deciles calculated by GAM detectability (window detection frequency). e, Distribution by genomic distance of SLICE interactions (red) and strong-and-common contacts (orange).