Fig. 3

Disease severity is linked to adenoma/adenocarcinoma and innate immune pathways. a Venn diagram shows the 712 UC severity genes overlapping the 5296 core UC signature with the 916 clinical severity and 1038 endoscopic severity genes differentially expressed between severe and mild cases (FC ≥ 1.5, FDR < 0.001). b Functional annotation enrichment analyses of the 712 UC severity genes. The full list of gene set enrichment results and P values are in Supplementary Dataset 2. Node colors are as in Fig. 1. c Computational deconvolution of cell subset proportions in controls and UC patients stratified by endoscopic severity Mayo subscore. Differences (ANOVA with FDR < 0.05 (*)) between Mayo 3 (severe, n = 71) and 1 (mild, n = 27) are shown for those cell types in Fig. 1. d Hematoxylin and eosin (H&E, 100×) staining of control (left) and UC (right) case with acute cryptitis (arrows), crypts that do not rest on the muscularis mucosa (bar), and marked surface villiform change (concave arrows). e Venn diagram shows the 187 villiform changes genes overlapping with severity genes. f H&E staining of UC case with acute cryptitis (arrow) and numerous eosinophils in the lamina propria (arrowheads). g Three genes that are associated with presence of >32 eosinophils/HPF in UC. h Frequency (percent of patient of the total per group) of mild (n = 54) and moderate-severe (n = 152) patients across histology severity scores (defined in Supplementary Table 2). **Chi squares p < 0.01. i Distribution of moderate-severe patients who did or did not achieve week 4 (WK4) remission across histology severity scores. UC ulcerative colitis. Box and whisker plot with central line indicating median, box ends representing upper and lower quartile, and whisker represent 10–90 percentile. Scale bar represents 50 μm