2.13 KEGG pathway analysis
The “enrichKEGG” function of the R package ClusterProfiler version 4.6.0 was applied to analyze biological pathways enriched in these 4 datasets with a p-value < 0.05. Only the genes differentially methylated and expressed at the promoter level, 1st exon or 1st intron were kept to carry out this analysis (number of hyper_downregulated genes = 184, hyper_upregulated = 58, hypo_downregulated = 328 and hypo_upregulated = 322). The ”emapplot” function implemented in the ”ClusterProfiler” package as well as the ”ggplot 2” and ”enrichplot” R packages were used to generate an enrichment map. The ”emapplot” function organizes the enriched terms into a network with edges connecting sets of overlapping genes. Overlapping sets of genes cluster together, making it easier to identify the functional module. The 5 KEGG pathways of each dataset with the most significant p-values have been represented. The proportion of clusters in the pie chart was determined by the number of genes.