Aire regulates a plethora of cytokines and chemokines in mTECs. (A) The Fitted model MA plot representing different genes (4002 down and 4366 up) regulated by Aire (gray dots) according to the fold change and average intensity at a 5% FDR using Illumina beadchip. (B) List of chemokine genes whose expression levels differ significantly between Aire^+/+ and Aire^−/− mTEC according to the Illumina beadchip analysis presented with fold change, average of the intensity, and adjusted P value. (C) Relative expression of Ccl1, Ccl3, Ccl6, Ccl7, Ccl8, Ccl9, Ccl11, Ccl17, Cxcl4, Cxcl13, Cxcl15, and Ccl25 was determined by quantitative real-time PCR on cDNA prepared from thymic CD45⁻MHC II^hi Ly51⁻ cells. Expression values are shown in relative to WT after normalization to Hprt. Data shown are the mean ± SEM of 3 independent experiments. A total of 6-8 individual thymi were pooled per experiment. Significance relative to WT: *P ≤ .05, **P ≤ .01; ns indicates not significant. (D) List of cytokine genes whose expression levels differ significantly between Aire^+/+ and Aire^−/− mTEC according to the Illumina beadchip analysis presented with fold change, average of the intensity, and adjusted P value.