Extended Data Fig. 2: Genome-wide hypermethylation of differentially methylated enhancer regions in PD neurons.
From: Epigenomic analysis of Parkinson’s disease neurons identifies Tet2 loss as neuroprotective
Differentially methylated regions at enhancers in prefrontal cortex neurons of 57 PD patients and 48 controls were identified (methylKit, sliding window: 1000 bp length, 50 bp step increment). a, Manhattan plot showing differentially methylated regions at enhancers in PD neurons (q < 0.05, logistic regression, adjusting for age, sex, postmortem interval, and neuronal subtypes). -log10(PValue) refers to the significance of region methylation change in PD, with the sign corresponding to the direction of change (red: hypermethylated, blue: hypomethylated region in PD). Threshold for genome-wide significance is q < 0.05 (black line, multiple testing corrected). Differentially methylated region in an enhancer of TET2 in PD neurons is highlighted. b, Proportion of hypermethylated (red) and hypomethylated (blue) regions at enhancers in PD. Enrichment determined by Fisher’s exact test with OR referring to the odds ratio and P = 10-38 significance of hypermethylation enrichment. Gray is all regions in the analysis (background). c, Intersection of the genes with differentially methylated cytosines or regions at enhancers in PD neurons. P = 10−16 is the significance of overlap determined by Fisher’s exact test.
