Figure 3

Gene-specific methylation changes were found at CpG sites across the genome. A) Unadjusted LME model p-value distributions for the effect of pre (0 hr) versus post (6-30 hr) exposure for FA, and that for DE. The uniform distribution expected by chance is indicated with horizontal dashed lines. Lack of positive skewing in the FA distribution indicated no association between FA exposure and differential methylation, whereas positive skewing in the DE plot indicated heavy association of DE exposure with differential methylation. B) Volcano plot of 2827 PCA hits. Negative log10 of fdr 10% adjusted p-values from LME modeling of the PCA hits were visualized against their corresponding ∆β values. Probes that were significant with a high confidence fdr of 10% were indicated in red. C) Distribution of ∆β obtained from subtracting pre-FA beta values from post-FA beta values, and from subtracting pre-DE beta values from post-DE beta values for the PCA identified probes that were significantly altered by DE exposure. ∆β from DE samples were much larger in magnitude than that from FA samples.