Fig. 4

HiCNAtra normalization successfully ameliorates the effects of CNVs on the MCF7 chromatin contact map. a Raw (top) and HiCNAtra-normalized (bottom) interaction heatmaps (500-kb bin) of MCF7 chr 1. Copy number track of chr 1 computed by HiCNAtra from MCF7 Hi-C data is shown on top. Each grey dot represents the copy number of a bin. The red line represents the copy number track where any amplitude transition indicates a new CNV region. Two amplified regions, CNV1 and CNV2, are shown that resulted in two off-diagonal block patterns (visible artifacts). b Post-normalized Hi-C interaction heatmaps (500-kb bin) of MCF7 chr 1 using ICE (top), CAIC (middle), and OneD (bottom) tools. The copy number track is shown as in (a). For the OneD tool, OneD + CN normalization module was used. c Visual comparison of the 1D signals of pre-corrected (raw) and post-corrected contact maps of MCF7 chr 1 using different Hi-C correction tools. The five panels show the raw and post-corrected 1D signals (red dots) using ICE, CAIC, OneD, and HiCNAtra tools, respectively. The blue line shows the moving average of the 1D signal. The black line with arrows represents a region showing a signal inversion effect. For each post-corrected 1D signal, the Spearman correlation (ρ) and standard deviation (s) are indicated next to each panel. d Bean plot of standard deviations per chromosome of 1D signal of cis contact map corrected by ICE (green), CAIC (teal), OneD (red), and HiCNAtra (blue) tools