Additional file 2 of Location-specific signatures of Crohn’s disease at a multi-omics scale

Additional file 2: Supplementary Figure S2. Features distinguishing CCD from ICD A) Enrichr plot generated from severity-controlled comparison of CCD to ICD (q-value = 8e-11). Of note, given the greater number of segments that can be scored for severity in CCD, this comparison is for presentation purposes only and does not truly represent a fair comparison to ICD (e.g. ICD patients could have more severe inflammation and still not score as high as CCD with less inflammation). B) Comparison of neutrophil-SES-CD score Spearman correlations in two single segment CD subtypes (ICD and rectal-only inflammation). Only significantly correlated proteins (p < 0.05, ICD = 17 proteins, Rectal = 14 proteins) were used in comparison. **** = p < 0.0001, Welch’s t-test. C) Comparison of neutrophil-SES-CD score Spearman correlations in two single segment CD subtypes (ICD and rectal-only inflammation) further controlled for SES-CD score (ICD mean = 6, CCD = 6.5). Top 10 most highly correlated proteins used. * = p < 0.05, Welch’s t-test. D) String-DB-generated network of combined inflammation-related cytokines and other proteins, filtered for high-confidence interactions (interaction score ≥ 0.7, see Supplementary Table 4) and proteins significantly increased in CCD compared to ICD. Grey dots represent imputed features, orange is features increased in CCD. E) Heatmap of mean dipeptide abundance per CD subtype. F) Plot of Log2 ratios of B. vulgatus in CD subtypes. No significance noted (ANOVA adjusted p > 0.05). ICD n = 25, CCD n = 17, ICCD n = 8. G) Plot of ICD and CCD Spearman correlation values generated by comparing B. vulgatus proteases (metaproteome features, log2-transformed) and SES-CD score. Welch’s t-test, p = 0.06.