Figure 3
From: Genome-wide methylation analysis identifies genes silenced in non-seminoma cell lines
Correlation between differential expression of over twofold and different degrees of differential CpG island methylation between seminoma and non-seminomas. Histograms showing the observed (blue) and expected (red) percentage correlation for each Δβ-value range for TCAM2 (seminoma) versus GCT44 (YST) (a), GCT27 (EC) (b) and NT2D1 (teratoma) (c). A Δβ-value of >0.65 or 0.7 consistently correlated significantly with a difference in expression of greater than twofold. While some lower Δβ-value categories also show significant association, statistical significance was reached at much smaller percentage levels of association due to a larger number of genes in those differential methylation ranges (see Figure 2 for details) (for example, comparing GCT44 to TCAM2, 152 genes exhibit Δβ-values between 0.2–0.25 with only 26% show a correlation with decreased expression (over a random expected association of 18%, but this achieves a P value <0.01). On the other hand, due to the small numbers of genes exhibiting some of the highest differential methylation values, these were not significantly associated with differences in expression, often despite a large percentage levels of association (for example, comparing GCT44 to TCAM2, seven genes exhibit a Δβ-values between 0.85 and 0.9 of which three (43%) show a correlation with decreased expression, but this does not achieve a significant P value). Significance of the Χ2-tests of association are shown (*P<0.05, **P<0.01, ***P<0.001) and the total number of genes in each category is displayed above the bar.
