Fig. 4
Characteristics of differentially methylated region in LGI1 encephalitis. A unsupervised hierarchical clustering based on the top 100 hyper-methylated and top 100 hypo-methylated CpG sites across 5 normal samples and 6 patients samples. Columns are samples and rows are CpG sites. B Principal component analysis of 5 normal samples and 6 patient samples based on methylation levels of differentially methylated CpG sites. C The proportion of all filtrated regions that are differentially methylated or not differential (up). The proportion of differentially hyper-methylated (red) or hypo-methylated (blue) regions (down). The proportion D and odds ratio E of differentially methylated regions (DMRs) in different chromosomes. The proportion F and odds ratio G of hyper-methylated (red) or hypo-methylated (blue) region in different chromosomes. The category H and odds ratio I of CGI locations for DMRs. The category J and odds ratio K of CGI locations for hyper-methylated (red) or hypo-methylated (blue) regions. The proportion L and odds ratio M of methylated regions correlated with the expression levels of genes in different chromosomes. Odds ratio was computed against the general distribution. DMRs, differential methylated regions; CGI, CpG island; shore, 0–2 kb from CpG island; promoter CGI, CGI located from 0 to 1000 bases upstream of the transcriptional start site (TSS) to 300 bases downstream of the TSS. Intragenic CGI, CGI located from 300th bases downstream of the TSS to 300th bases upstream of the transcriptional end site (TES); transcript CGI, CGI located from 300th bases upstream of the TES to 300th bases downstream of the TES; intergenic CGI, CGI located from 300th bases downstream of the TES to 1000th bases upstream of the TSS of next gene