Fig. 2: Raichu identifies thousands of transcription-related loops missed by ICE.

HiCCUPS was used for loop detection. a Venn diagram showing the overlap of loops detected by ICE and Raichu in GM12878 cells. b Violin plots comparing the sizes of ICE-specific (n = 1449), Raichu-specific (n = 14,989), and shared (n = 13,997) loops detected by both methods. 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. c Comparison of contact signals in an example genomic region normalized by ICE or Raichu. Contact heatmaps are shown alongside gene annotations, RNA-seq profiles, and ChIP-seq signals for selected transcription factors and histone modifications. Black circles indicate detected loops, yellow bars mark loop anchors detected by both ICE and Raichu, and blue bars denote Raichu-specific anchors. d Proportions of promoter–promoter (P–P), enhancer–enhancer (E–E), and promoter–enhancer (P–E) loops among ICE-specific, Raichu-specific, and shared loop sets. e Fraction of loop anchors bound versus fold enrichment for 132 transcription factors and 10 histone modifications, with colors indicating loop categories. f ChIP-seq profiles of selected transcription factors and histone modifications centered on both anchors of each loop, grouped by loop category. Each row represents one loop. g Overlap of each loop category with orthogonal ChIA-PET and HiChIP interactions. h APA plots for ICE-specific and Raichu-specific loops in ICE- and Raichu-normalized Hi-C maps. Source data are provided as a Source Data file.