Fig. 3

Cell type-specific gene expression changes in T1DM. a Total number of unique upregulated and downregulated DEGs in 14 peripheral immune cell types: 46 T1DM samples vs. 31 healthy. b Bar plot representing the number of DEGs within each cell type, with colored segments indicating the number of cell types that share the same DEG. c Heatmap of T1DM vs healthy log2 (fold-change) of 1784 DEGs (\(691+1093\)) across all immune cell types. Genes are clustered by their fold-change vectors using k-means. Each gene cluster is annotated by the most significantly enriched Gene Ontology (GO) term. d Gene set enrichment analysis (GSEA): dot plot of top shared and cell type-specific biological processes enriched in DEGs of each PBMC cell type, colored by normalized enrichment score (NES). Dot size: \(-log10\) (FDR q-value). e Differential regulon activity: heatmap of transcription factor regulons with increased or decreased activity in T1DM (union of top 5 regulons in each of the 13 peripheral immune cell types). Color indicates \(-log10\) (FDR q-value) of regulons upregulated (yellow) and downregulated (purple) in T1DM. f Overlap between GSEA leading-edge genes and significantly differential regulons in 6 peripheral cell types. Color indicates \(-log10\) (FDR q-value) of overlap (Fisher’s exact test)