Fig. 2

CpG Statistical Comparisons Based on a Likelihood-Ratio-Test of a One Way ANOVA contrast. a Volcano plot with the frequency profile of p-values. Data from the 1.47 million CpG sites in common across all samples are plotted. The x-axis is the log value for the fold-change (ratio) of CP to non-CP CpG site methylation values and the y-axis is the log FDR value (gray = not significant, orange = p-value significant, and red = p-value after FDR significant). b Heatmap Clustering of the top 200 CpG sites selected based on statistical p-value. There were 6588 CpG sites that were significantly different (p < 0.05 after false-discovery rate correction). Hierarchical clustering based on % methylationwas employed using the 200 CpG sites with the lowest p-values. Quantitative differences in CpG site methylation by diagnosis were apparent. Each row represents the score for a single CpG site across all subjects