Comparative analysis of Aire-regulated genes in rat and mouse. (A) A volcano plot comparing mTEC gene expression in Aire-deficient and control animals. Red and blue dots indicate up- and down-regulated genes, respectively. Data were obtained from a single experiment with 4 Aire-deficient (KO) and 3 control (HE) rats per group. (B) Gene ontology (GO) enrichment analysis of Aire-regulated (i.e., downregulated) genes in rats shows enrichment of pathways related to defense response. Only 10 most statistically significant GO terms are shown. (C) Gene expression levels as measured by qPCR of ISGs in whole thymi, spleens, and lymph nodes of 1–1.5-mo-old (young) and >7-mo-old (old) Aire-deficient (KO) and control (HE) rats (n = 5–6, combined from two or more experiments). (D) Principal component analysis of Aire-regulated genes in rat and mouse shows a species-specific effect of Aire. (E) Heatmap showing normalized scaled gene expression of Aire-regulated genes in rat and mouse. The genes were clustered into four groups using K-means clustering. Mouse and rat TRA genes are indicated on the right. (F) GSEA comparing the degree of ISG downregulation in Aire-deficient rats and mice. Color scale shows the normalized enrichment score (NES) and dot size represents -log10 of the associated P value. (G) Running enrichment score (ES) for ISGs in each rat and mouse dataset. (H) Heatmap showing log fold changes for ISG genes in rat and mouse datasets. (I) Gene expression levels as measured by qPCR of ISGs in whole thymi of 1.5-mo-old Aire-deficient (KO) and WT mice (*P < 0.05, n = 5 for both KO and WT, combined from two or more experiments). In C and I symbols indicate individual animals, horizontal lines with whiskers indicate mean values with SEM. All reported P values are based on t tests. Statistical significance is indicated as follows: ****P < 1e-4, **P < 0.01, *P < 0.05, and ns (not significant) for P ≥ 0.05.
Figure 4.

Comparative analysis of Aire-regulated genes in rat and mouse. (A) A volcano plot comparing mTEC gene expression in Aire-deficient and control animals. Red and blue dots indicate up- and down-regulated genes, respectively. Data were obtained from a single experiment with 4 Aire-deficient (KO) and 3 control (HE) rats per group. (B) Gene ontology (GO) enrichment analysis of Aire-regulated (i.e., downregulated) genes in rats shows enrichment of pathways related to defense response. Only 10 most statistically significant GO terms are shown. (C) Gene expression levels as measured by qPCR of ISGs in whole thymi, spleens, and lymph nodes of 1–1.5-mo-old (young) and >7-mo-old (old) Aire-deficient (KO) and control (HE) rats (n = 5–6, combined from two or more experiments). (D) Principal component analysis of Aire-regulated genes in rat and mouse shows a species-specific effect of Aire. (E) Heatmap showing normalized scaled gene expression of Aire-regulated genes in rat and mouse. The genes were clustered into four groups using K-means clustering. Mouse and rat TRA genes are indicated on the right. (F) GSEA comparing the degree of ISG downregulation in Aire-deficient rats and mice. Color scale shows the normalized enrichment score (NES) and dot size represents -log10 of the associated P value. (G) Running enrichment score (ES) for ISGs in each rat and mouse dataset. (H) Heatmap showing log fold changes for ISG genes in rat and mouse datasets. (I) Gene expression levels as measured by qPCR of ISGs in whole thymi of 1.5-mo-old Aire-deficient (KO) and WT mice (*P < 0.05, n = 5 for both KO and WT, combined from two or more experiments). In C and I symbols indicate individual animals, horizontal lines with whiskers indicate mean values with SEM. All reported P values are based on t tests. Statistical significance is indicated as follows: ****P < 1e-4, **P < 0.01, *P < 0.05, and ns (not significant) for P ≥ 0.05.

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