Extended Data Fig. 1: I2 subjects are inflamed.

a, Histologically-scored inflammation in the right colon of patients without a history of dysplasia, separated by transcriptionally-determined cluster. 0 = no diagnostic abnormality, 1 = quiescent inflammation, 2 = mild inflammation, 3 = moderate inflammation, 4 = severe inflammation. Significance determined by two-sided, unpaired Wilcoxon test without adjustment for multiple comparisons. b, Single sample gene set analysis (ssGSEA) score for the Inflammatory Response gene set (HALLMARK_INFLAMMATORY_RESPONSE, Molecular Signatures Database v7.5.1) calculated from the right colon tissue transcriptome of patients without a history of dysplasia, separated by transcriptionally-defined cluster. Significance determined by two-sided, unpaired Wilcoxon test without adjustment for multiple comparisons. n = 34 I2, 26 I1, 156 U (a, b). c, Distribution of subjects with no history of dysplasia across clusters, statistical significance determined by two-sided Fisher t-test. d, Volcano plot summarizing the differentially expressed gene analysis of PSC I2 subjects with right-sided dysplasia versus PSC I2 subjects with no history of dysplasia (n = 5 PSC I2 with dysplasia, 17 PSC I2 without dysplasia). 0 genes passed the threshold of significance (red dashed line, adjusted p-value > 0.05), suggesting that the transcriptional profile of PSC I2 subjects is identical whether or not the patient has right-sided dysplasia. e, Histologically-scored inflammation in patients with PSC and IBD that have dysplasia, separated by the location of dysplasia (n = 6 PSC-right, 7 IBD right-sided dysplasia, 9 IBD left-sided dysplasia. Significance determined by two-sided, unpaired Wilcoxon test without adjustment for multiple comparisons. Center line represents the median value; hinges indicate the 1st and 3rd quartiles; upper and lower whiskers extend to the largest and smallest values that are within 1.5 times the interquartile range from 1st and 3rd quartiles, respectively (a,b,e).