Fig. 1

Identification and annotation of Differentially Methylated Regions (DMRs). (A) The volcano plot shows the DMRs. The x-axis represents the log2 fold change (FC) of methylation, and the y-axis represents the -log10(p-value). The regions with a p-value < 0.01 and |log2(FC)| >= 2 were selected as differentially methylated. The yellow points represent the hypermethylated regions (7,095), the blue points represent the hypomethylated regions (212), the dark gray points represent the not significant regions. (B) Principal Component Analysis of TCGA-BRCA methylation data overlapping the DMRs. The red points represent the primary tissue samples, while the blue ones represent the solid tissue normal samples. (C) Proportion of DMRs according to Genic Annotations. The distribution of DMRs across the 3UTRs (3’ untranslated regions), CDS (coding DNA sequences), enhancers_fantom (enhancers from FANTOM5), 5UTRs (5’ untranslated regions), 1to5kb (1 to 5 kb regions upstream of transcription start site, TSS), promoters (regions with a length of less than 1 kb upstream of TSS) were explored. (D) Proportion of DMRs according to CpG Annotations