Fig. 1

Heat map and circular plot visualization of Hi-C data. a Hi-C interactions among all chromosomes from G401 human kidney cells, as plotted by my5C. The green arrow points to aberrant interchromosomal signal in the Hi-C matrix, possibly caused by a rearragement event. b Heat map visualization illustrating the bipartite structure of the mouse X chromosome, as plotted by Hi-Browse, using in-situ DNase Hi-C data [49]. c Heat map visualization of a 3 Mbp locus (chr4:18000000-21000000) reveals the presence of loops that coincide with CTCF binding sites, validated by CTCF peaks shown on the top and left of the heat map. Computationally annotated loops are displayed as blue squares in the heat map. This heat map was produced by Juicebox, using in-situ Hi-C data from the GM12878 cell line [28]. d Circular plot of the bipartite mouse X chromosome, which shows a striking depletion of arcs between the two mega-domains, the locus that separates the mega-domains is shown by a green arrow. The plot was generated by the Epigenome Browser