Fig. 5: Higher complexity contacts are more frequently captured by GAM.
From: Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C
a, Interaction complexity: simple interactions involve only a few genomic regions, while complex interactions involve many genomic regions at once. In Hi-C, ligation events connect two pieces of DNA; therefore, pairwise contacts can be directly determined while measurement of higher-order contacts may be affected by competing ligation events resulting in dilution effects (1, arrow). Co-segregation determined through GAM is not affected by the number of elements (2). b, Number of triplets formed by Hi-C-preferred, common or GAM-preferred regions in the A compartment (left) or the B compartment (right). c, Number of triplets formed by genomic windows that are positive for a feature, shown genome-wide and within Hi-C-preferred, common or GAM-preferred regions. Bars mark the 25%, 50% and 75% quantiles; labels give the total number of windows in each group. d, Relationship between pairwise Hi-C ligation frequency, pairwise GAM normalized linkage and the number of triplets. e, Hi-C ligation frequency of 1 Mb pairwise contacts that have a similar GAM normalized linkage, colored by number of triplets (zoomed subset of d). f, Overlap of triplet contacts identified by SLICE from GAM data and inferred from Hi-C by using the strongest 2% based on transitivity. g, Overlap of triplets found by SLICE in GAM data and triplets derived from 3D models from single-cell (sc)-Hi-C.
