Supplementary Figure 6: RNA-seq analysis (supplementary information for Fig. 5)

(a) Plot of gene expression (as log₂ normalized read count) in control T naive versus STAT5b-CA T naive cells (i.e., naive CD4⁺ T cells from Foxp3^Cre-ERT2Rosa26^Stat5bCA mice). The diagonal lines indicate fold change of at least 1.5× or 0.67× fold. Significantly up- and down-regulated genes (defined as genes with at least 1.5× or 0.67× fold change, adjusted P-value ≤ 0.05, and expression above a minimal threshold based on the distribution of all genes) are colored red or blue, respectively, and their numbers are shown. (b) Volcano plot showing log₁₀ FDR-adjusted P-values versus log₂ fold change between STAT5b-CA and control T_reg cells. Genes that fall outside of the x- or y-axis range of this plot are shown on the axes as empty triangles. The vertical and horizontal gray lines indicate 1.5× or 0.67× fold change (±log₂ 1.5 = ±0.58) and P = 0.05 (−log₁₀ 0.05 = 1.3), respectively. (c) Network analysis of GO term enrichment among significantly downregulated genes in STAT5b-CA expressing vs. control T_reg cells. Downregulated genes were analyzed for over-represented GO terms using BiNGO in Cytoscape, and the resulting network was calculated and visualized using EnrichmentMap. Groups of similar GO terms were manually circled. Edge thickness and color are proportional to the similarity coefficient between connected gene sets. Node color is proportional to the FDR-adjusted P-value of the enrichment. Node size is proportional to gene set size.