2.8 Correlation analysis of genome-wide DNA methylation and gene
expression
In order to reveal the complex regulation of gene expression by DNA
methylation, violin plots were generated with the ggplot2 R package
(version 3.3.6). Correlations between DNA methylation and gene
expression levels were measured using Spearman’s rank correlation
coefficient. Gene expression levels were based on counts, normalized
according to the DESeq2 method (Anders et Huber 2010), and then divided
into deciles of an equal number of genes ranging from the least (decile
1) to the most expressed (decile 10) genes. DNA methylation levels were
based on the beta-value indicated in the BED files. DNA methylation
levels in specific genomic regions were represented relative to the gene
expression levels.