Fig. 2: Comparison of thymic immune cell profiles across wild-type (WT) and Aire-deficient (AireC313X−/−) mice.
From: Aire-dependent interferon signalling shapes thymocyte maturation and central tolerance in mice
a UMAP plots of immune cell populations in AireC313X−/− and WT mice. b Proportion of cells in clusters compared across AireC313X−/− and WT (n = 4 per genotype, Wilcoxon rank sum test with Benjamini–Hochberg correction, ns). Error bars in bar plots indicate standard deviation. c Number of significantly differentially expressed genes (DEGs) per cluster, red marks upregulated and blue downregulated DEGs in AireC313X−/−. d Heatmap displaying log2fc values for selected DEGs across AireC313X−/− and WT, for full overview see Supplementary Data 1.3. Colour scale red: upregulated and blue: downregulated genes in AireC313X−/−. Gene names coloured by corresponding GO terms from Fig. 2e, f: red: response to type I IFN/IFN-beta, yellow: response to virus, blue: antigen processing and presentation, purple: regulation of T cell activation. Top GO terms enriched among e downregulated genes and f upregulated genes for clusters with more than 10 DEGs total. As many of the GO terms showed considerable degree of redundancy, we only show terms we deemed most relevant, for full overview see Supplementary Data 1.4 and 1.5). GeneRatio indicates the ratio of genes in term among DEGs, while log10 for adjusted p values are indicated by the colour scale (over-representation test, a version of Fisher's exact test with Benjamini–Hochberg correction).
