Fig. 2: Heterogeneity of the EL gene expression allows classification of duodenal biopsies into non-inflamed, mild inflammation, and severe inflammation.

A Heatmap of DE gene expression (n = 1862) across samples. Rows represent genes, columns represent samples. Genes are clustered into four clusters and three groups, shown alongside CeD condition, Marsh score, and APOA4:KI67 ratios. Scaled and centred gene expression is displayed as Z-scores. B Pathway enrichment analysis of gene clusters using Reactome. Top five pathways per cluster (y-axis) are shown with the number of contributing genes in brackets. C Statistical comparison of APOA4:KI67 ratios, a crypt length indicator, using Dunn’s test with Bonferroni correction (adjusted p < 0.01). D Correlation of representative DE genes from each cluster [1,2,3,4] with APOA4:KI67 ratios. Each plot shows VST-transformed gene expression vs. APOA4:KI67 ratio, with dot colour indicating CeD condition. (E) Overview of significant DE genes resulting from comparisons between Group 2 UCD and CTRL, within TCD (Group 2 vs 1), and within UCD (Group 3 vs 2) on the x-axis. Directions of DE are indicated by colour: upregulated (red) and downregulated (blue). See Supplementary Table 4 for complete gene lists. F Overlap of DE genes from all comparisons, divided into upregulated (left) and downregulated (right) sets, visualized with Euler diagrams (top) and Upset plots (bottom).