PMC

Diagnostic differences in the DNA methylation levels of GRIA4 and ASTN2. The x axis represents diagnostic groups (control and schizophrenia), and the y axis represents DNA methylation levels (log2 ratio of methylated and unmethylated probe intensities). The lines in the bar graph indicate the median, and the bars (whiskers) represent the minimum and maximum values after the removal of the outliers. The CpG sites of the GRIA4 (cg19343464) and ASTN2 (cg00121640) showed significantly higher DNA methylation in patients with schizophrenia than in controls (p = 3.55 × 10⁻⁷ and p = 1.09 × 10⁻⁶).

Cis-association of a SNP with DNA methylation. The x axis represents three genotypes of each SNP (1/1 red, 1/2 green, and 2/2 blue, where 1 = A or T allele and 2 = G or C allele), and the y axis represents DNA methylation levels. The lines in the bar graph indicate the median, and the bars (whiskers) represent the minimum and maximum values after the removal of the outliers. rs7914558 was associated with DNA methylation status at cg15439196 in the CNNM2 gene (Bonferroni corrected p = 1.74 × 10⁻²).

Diagnostic differences in DNA methylation. The x axis represents magnitude of a change (beta value) between controls and schizophrenia subjects calculated by linear regression analysis in 216 samples. The y axis represents −log 10 p-values. Each dot represents an individual CpG site (a total of 25,156 CpG sites). Red dots represent 107 CpG sites that showed significant diagnostic differences between schizophrenic subjects and controls (5% Bonferroni correction). Magnitude of change >0 corresponds to higher methylation in patients with schizophrenia than in controls, whereas magnitude of change <0 corresponds to lower methylation in patients with schizophrenia than in controls. Of these 107 CpG sites, 79 sites (73.8%) demonstrated higher methylation in patients with schizophrenia than in controls.