Fig. 6

Cell-type specific looping interactions identified from Hi-C using 3DeFDR-HiC. a Reference heatmaps of relative Hi-C interaction frequency (Observed) for the Sox2 region and two zoom-in views of loops involving the Sox2 gene. Boxes 1, 2, and 3 highlight areas of differential looping. b Reference interaction score heatmaps of the same genomic regions shown in a. c Distance-dispersion relationship in the ES condition in the Bonev et al. Hi-C dataset. The orange dots show the estimated negative binomial dispersion parameter at each distance scale. The purple line represents a LOWESS smoothing of the orange points. The red dashed line shows the effective dispersion of the Poisson distribution for comparison. d MA plot of the differential loop analysis comparing the ES and NPC conditions in the Bonev et al. Hi-C dataset. The x- and y-axes represent the average log interaction frequency and the log fold change across cell types, respectively, computed on observed Hi-C counts normalized for both locus specific biases and sequencing depth differences. The densities of non-loop, constitutive, and differential (called by our method at an FDR threshold of 1%) pixels are shown in different colors as indicated in the legend. e Heatmaps of final loop cluster classifications for each genomic region called by 3DeFDR-HiC at an FDR threshold of 1%