Fig. 5: Raichu detects unique differential loops associated with transcriptional regulation.

a Comparison of Hi-C contact maps, RNA-Seq, GATA3 ChIP-Seq, and H3K27ac ChIP-Seq signals between wild-type (C/C) and engineered (A/A) GM12878 cells. The left panel shows ICE-normalized Hi-C maps, and the right panel shows Raichu-normalized maps. Black circles indicate detected loops, and the anchors of a Raichu-specific A/A loop are highlighted in yellow. b Venn diagram showing the overlap of loops detected by ICE and Raichu in C/C and A/A cells. c Loop size distributions for C/C-specific and A/A-specific loops unique to ICE or Raichu. The number of loops in each group is: ICE-specific C/C (n = 245), Raichu-specific C/C (n = 937), ICE-specific A/A (n = 65), and Raichu-specific A/A (n = 249). For box plots overlaid on each violin, the center line indicates the median, the box limits represent the upper and lower quartiles, and the whiskers extend to 1.5 times the interquartile range. d APA plots for C/C-specific and A/A-specific loops unique to ICE or Raichu, shown in both C/C and A/A Hi-C maps. e Counts of promoter–enhancer (P–E), enhancer–enhancer (E–E), and promoter–promoter (P–P) loops within the indicated loop categories. f H3K27ac and GATA3 binding profiles centered on loop anchors for the indicated loop categories. Gray and black lines represent signal profiles from C/C and A/A cells, respectively. g Quantile-normalized transcription levels in C/C versus A/A cells for genes linked to GATA3-bound enhancers via the indicated loop categories. In each box plot, the center line indicates the median, the box limits represent the upper and lower quartiles, and the whiskers extend to 1.5 times the interquartile range. P values were calculated using a two-sided Wilcoxon signed-rank test. n denotes the number of genes in each comparison. Source data are provided as a Source Data file.