Extended Data Fig. 5: Gene and gene ontology pathways that are shared and different across disease states in Epsilon-1, Epsilon-2, and Immune cells.

(a-c) (Left) For each cell type, Venn diagrams indicate the numbers of upregulated and downregulated genes, as well as overlapping genes, across the two disease states. Circles indicate the numbers of genes that are ‘T1D enriched’ or ‘AAb enriched’. p-values presented are the results of hypergeometric CDF tests (one-tailed test for overrepresentation). (Middle) For each cell type, displayed are gene ontology pathways that are shared across T1D and AAb⁺ cells when compared to Control cells (top) or pathways that are differently enriched in T1D cells vs AAb⁺ cells (bottom). The top 20 clusters are displayed and a stringent cut-off of 1e-6 was applied to determine significant gene ontology pathways. (Right) Heatmaps displaying the degree of gene expression changes of genes (rows) that are shared (top) or differential (bottom) across AAb⁺ and T1D disease states. (d) GSEA analysis plots of FDR q-value vs Normalized Enrichment Score. For both ductal populations, Ductal-1 and Ductal-2, T1D cells were compared to AAb⁺ or Control cells to determine differentially enriched gene sets. Demarcated in red and labeled are signatures of interest.