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).