Fig. 3

Characterization of cfDNA-derived DNA methylation landscapes in ALS. (A) Bar graph showing average genome-wide mCG levels in ALS and control groups. No significant difference of methylation levels was observed between groups. (B) Metagene plots showing mCG (top) levels across transcriptional start sites (TSS), transcriptional end sites (TES) and RefSeq gene bodies. Ten kb upstream and downstream of given genomic features were plotted. (C) Identification of DMRs between ALS and control groups (top), with a heatmap (bottom) visualizing the methylation profiles of the identified DMRs. (D) Genomic annotation of the identified DMRs on their percentage of each genomic feature. (E) Proportion of ALS-related DMRs within CpG islands (CGIs), CpG shelves, CpG shores, and other genomic regions. (F) Top: Proportion of hypermethylated DMRs and hypomethylated DMRs on their percentage of each genomic feature. Bottom: Fold enrichment of DMRs over genomic background. (G) GO and KEGG pathway analysis of DMR-associated genes to explore their functional relevance to ALS