Fig. 2: Identification of cancer-associated CpGs and differential expression analyses of the associated genes.

Results from the overlap step of the pipeline and differential expression analyses of the genes associated with the enriched CpGs in (a) breast cancer (BrCa) and (b) prostate cancer (PrCa). Due to the unavailability of healthy prostate methylation data, the overlap step in PrCa did not include differential methylation between tumour and healthy tissues. For differential expression analysis, the CpGs were annotated to genes through ANNOVAR-, distance- and eQTL-based approaches. The differential expression was conducted in the TCGA gene expression dataset using DESeq2 for ANNOVAR- and distance-based genes and using the GWAS summary statistics and FUSION for eQTL-based genes. Up and Down for gene in the matrix refer to up- and downregulated gene expression while Hypo and Hyper for CpGs indicate hypo- and hyper-methylation, respectively. CpGs cytosine-phosphate–guanine sites, DEGs differentially expressed genes, DM differentially methylated, NAT histologically normal tissue adjacent to the tumour.