Fig. 4: Epithelial cell heterogeneity and the interaction with immune cells.

a, Expression heatmap for the top 50 upregulated DEGs in 24 epithelial cells of 15 selected gastrointestinal tissues, showing significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways for the clustering module (left), specific TFs (middle) and corresponding tissue anatomical structures and cellular composition (right). b, Volcano plot illustrating the DEGs between paratuberculosis-seropositive and healthy cattle. DEGs were identified based on FDR < 0.05 and log₂(fold change) > 1 using edgeR’s two-sided exactTest. c, Box plot showing the module scores of 17 disease-associated and 56 health-associated upregulated genes in epithelial cells of the intestine (n = 5), calculated using the AddModuleScore of Seurat. The central band in the box plot represents the median, the box boundaries represent the 25% to 75% percentiles, and the whiskers extend 1.5 times the IQR. A two-sided Wilcoxon rank-sum test was used. d, Bubble plot showing ligand–receptor pairs between GCs and immune cells, which were shared in at least four intestinal segments. e, t-SNE visualization of seven GC subtypes. Cells are color-coded according to cell subtype. f, Heatmap showing the top 20 upregulated DEGs and their markers for each GC subtype. The bar chart displays their GO terms and KEGG pathways using single-sample gene set enrichment analysis (GSEA). g, Heatmap representing the tissue distribution of GC subtypes; ORs were calculated and used to indicate preferences. **OR > 1.5 and FDR < 0.01. h, Heatmap displaying the signature scores of tuberculosis and paratuberculosis candidate genes from the Animal Quantitative Trait Loci (QTL) and KEGG databases across GC subtypes. i, Scatter plot highlighting tissues and GC subtypes associated with human IBD and CD using GWAS enrichment analysis with LDSC. j, Violin plot representing the expression of key ligand–receptor genes in GC subtypes and immune cells.