Comparison of contact maps between ChIA-PET and Hi-C at multiscale. (A) Normalized inter-chromosomal contact heat maps between all pairs of chromosomes. The ChIA-PET and Hi-C show similar heat maps with a correlation coefficient of 0.73. The boxplot shows the normalized contact frequencies distribution. The color bar indicates the enrichment of contact frequency, where red indicates enriched contacts and yellow indicates depleted contacts. (B) The intra-chromosomal contact heat maps for Chr 3. The ChIA-PET and Hi-C showed similar contact heat maps with a correlation value of 0.67. The chromosome was binned at 1-Mb resolution. The boxplot shows the contact frequencies distribution. The color bar indicates the enrichment of contact frequency. Colors are as in A. (C) The contact heat maps of topological associated domains (TADs). The heat maps of two TADs display similar patterns between ChIA-PET and Hi-C. The bottom panel shows the interaction loop views for CTCF and Pol II PET clusters, respectively. Interaction hotspots are marked with ovals in contact heat maps and are highlighted with purple bars in 2D track views. TADs were binned at 50-kb resolution. CTCF and Pol II ChIA-PET data were combined to generate the heat maps.