3.3 Correlation analysis of gene expression and DNA methylation levels in different genomic contexts
In the promoters, gene expression levels were negatively correlated to DNA methylation levels (R = -0.22, p-value = 2.2e-16) (Fig. 4). In the first exons, this negative correlation was even stronger (R = -0.42, p-value = 2.2e-16) and we observed less genes with intermediate methylation levels. Most genes exhibited strong methylation levels (>60%) had low gene expression levels (from first to 3rd decile). We also observed a negative correlation between gene expression and DNA methylation levels in the first introns (R = -0.34, p-value = 2.2e-16) with a similar pattern than in promoters. Interestingly, lower methylation levels (<40%) were observed for highly expressed genes (from 7th to 10th decile). In contrast, when considering the rest of exons and introns, no significant correlation was found between DNA methylation and gene expression levels (R = 0.01, p-value = 0.127).