Fig. 3

CREaTor captures hierarchically higher-order genome organizations. a Example genomic regions showing the similarity between attention matrix (above the diagonal) and Hi-C contact matrix (below the diagonal). Orange boxes indicate TAD domains. b Average insulation scores across the K562 genome at 10-kb resolution calculated from attention matrix and Hi-C. Blue line and left y-axis: insulation scores of attention matrix. Pink line and right y-axis: the insulation scores of Hi-C. Solid lines indicate insulation scores over K562 TAD boundaries and dashed lines indicate insulation scores over GM12878 boundaries. The x-axis is centered on TAD boundaries. c Upper panel: Statistics of attention weights between CTCF-bound element pairs with different topological relationships. Center line, median; box limits, upper and lower quartiles; whiskers, 1.5 × interquartile range. Lower panel: illustration of CTCF-bound element pairs used for the analysis. The red triangle represents TAD domains called from the Hi-C matrix (blue). d Average attention scores between elements without normalization. p-value is calculated with Mann–Whitney U test