Supplementary Figure 3: Foxp3 acts predominantly as a transcriptional repressor.

(a) Peak-rank enrichment of Foxp3 binding for differentially expressed genes. Down- and up-regulated gene sets (blue and red, respectively) are shown at various q-value cutoffs. The y-axis shows the odds ratio of enrichment of the hypergeometric test to estimate the extent of overlap between differentially expressed genes and Foxp3 target genes. (b) Cumulative distribution of Foxp3 target gene expression changes in rTreg vs. Foxp3^GFPKO and aTreg vs rTreg cells. (c) Overlap of differentially expressed genes with Foxp3 bound genes. Experimental conditions are described in the main text. Odds-ratio (OR) enrichment value and hypergeometric p-values are shown. (d) Foxp3-binding at distal upstream and first-intron sites is associated with increased repression of Foxp3-target genes. Cumulative distribution (y-axis) of Log₂ expression fold change (x-axis) for aTreg vs Teff cells (top row) and rTreg vs Foxp3^GFPKO cells (bottom row).