Fig. 4

PReLIM increases power and coverage of WGBS datasets. a Differentially methylated regions (DMRs) identified in the mouse neuron vs. glia WGBS dataset before and after imputation. b, c Heatmap showing the top 10 GO biological process terms for DMRs with b lower methylation in neurons and c lower methylation in glia, before and after imputation by PReLIM; analysis was conducted using GREAT, color represents the -log10 q value. PReLIM generally increases the statistical significance of the GO terms. d Examples of tanghulu plots showing WGBS reads at DMRs identified only post-imputation; rows and columns represent reads and CpG sites, respectively. Filled and empty circles represent methylated and unmethylated CpGs. e Examples of bisulfite pyrosequencing results of DMRs identified only post-imputation. Each point represents a single CpG site in the pyro assay, within the DMR. Horizontal dotted lines indicate average cell type-specific methylation across the DMR, from the WGBS data following PReLIM imputation. DMR positions relative to genes are depicted below each plot. Black box indicates DMR location, blue gene-body schematic is oriented 5′ to 3′