Fig 1: Comparative analysis of siRNA effects on the transcriptome and epigenome.a Left: Number of DEGs for each siRNA treatment (FDR < 0.01). Right: Correlation heatmap based on the Simpson index (showing overlap among top-ranked 1000 DEGs) for all sample pairs. b Clustering of all top-ranked DEGs (rows) and samples (columns) based on the overlap of up- and downregulated genes. The significant GO terms are also shown (left). See Fig. S6 for the full list of GO terms. c Log-scale relative enrichment of ChIP-seq peaks (left) and Hi-C loops (right) at the TSSs of DEGs in the clusters corresponding to (b) against all DEGs. * indicates the statistical significance of the enrichment or depletion (p < 0.01, two-tailed permutation test, n = 1000). d ChIP-seq distribution (–log10(p), two-tailed binomial test, 100-bp bin) among top-ranked DEGs (BMP6, SSBP2, and TNFRSF19). The significantly enriched regions (p < 10–4) are highlighted in red. Red and black arrows (bottom) indicate CTCF-independent and -dependent Rad21 peaks, respectively. e The relative enrichment of Rad21 peaks after depletions and of Smc3ac around genes, as compared with Rad21 (control). **p < 0.001; ***p < 0.0001, two-tailed Fisher’s exact test against control. The exact p-values are shown in Source Data file. Source data are provided as a Source Data file.