Fig. 3

A Representation of the overlap between cfDNA DMRs in MTLE and hippocampal DMRs in MTLE. The sets of DMRs overlapped separately in relation to the type of DMR (promoter, gene, CGI) and the methylation behaviour (hypermethylated and hypomethylated). Red bars and lines indicate the overlap of DMRs with coincidence in the direction of change. B Heatmap matrix representation of the p values associated with the Fisher’s exact test of the overlaps between DMRs in cfDNA and in the hippocampus. C Representation of the overlap between cfDNA DMRs in MTLE and neocortical DMRs in MTLE. The sets of DMRs overlapped separately in relation to the type of DMR (promoter, gene, CGI) and the methylation behaviour (hypermethylated and hypomethylated). Red bars and lines indicate the overlap of DMRs with coincidence in the direction of change. D Heatmap matrix representation of the p values associated with the Fisher’s exact test of the overlaps between DMRs in cfDNA and in the neocortex. E–G Graphical representation of the DNA methylation of the individual probes in cfDNA, hippocampus, neurons vs. blood cells, and glia vs. blood cells, and DNase-seq hypersensitivity in brain tissue and blood cells, corresponding to the DMRs located at the promoter of the PM20D1 gene (E), at the chr8:145,008,908–145,009,407 CGI (F) and at the chr7: 70,254,894–70,255,986 CGI (G). DNA methylation is presented as beta values. Beta diff is the mean difference of the beta values of all individual probes in the DMR for each comparison. FDR corresponds to the Bonferroni-adjusted p value emerging from the mCSEA DMR calculation. The genomic location of each DMR is highlighted by a red line in the respective chromosome. The DMRs (green) and the individual probes (orange) are presented in relation to the annotated genes in the UCSC Ref Seq