Extended Data Fig. 10: Compartment-association of GAM-specific contacts.
From: Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C
a, PCA eigenvalues from GAM and Hi-C for mouse chromosome 1. b, Correlation heatmap for GAM and Hi-C eigenvalues. A small subset of windows assigned to the A compartment by GAM (positive eigenvalues) are assigned to the B compartment by Hi-C (negative eigenvalues). Value histograms indicate that Hi-C eigenvalues are clearly bimodal distributed while GAM finds an increased number of eigenvalues in the transition zone. c, Agreement between GAM and Hi-C compartment calls for GAM-preferred (left), Hi-C preferred (middle) and common (right) regions. d, Absolute number (left) and enrichment over random background (right) of compartment combinations observed in the sets of Hi-C-specific contacts (blue) and GAM-specific contacts (red). Compartment definitions of 1Mb resolution were obtained from Hi-C data (top) or GAM data (bottom); * P < 0.05, ** P < 0.01, empirical test, n = 500 contact permutations.
