Figure 4 | Scientific Reports

Figure 4

From: Etiology matters – Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy

Figure 4

Correlation between methylation and gene expression.

(a) - Examples of GSEA enrichment profiles of association between gene expression and alterations in promoter methylation, A strong association (FDR < 0.25 was considered significant) was observed between increased promoter methylation and gene activation in the TBI model, between decreased promoter methylation and gene repression in the focal amygdala stimulation model and between decreased promoter methylation and gene activation in the systemic pilocarpine model. ES - enrichment score, PRL - pre-ranked list, FDR - false discovery rate. (b) - Gene set enrichment analysis (GSEA) presenting associations between gene expression and methylation changes in different genomic features in three epilepsy models. The results are presented as false discovery rates of nominal p-values of gene sets of increased or decreased methylation events at promotors (5 kb upstream of transcription start), CpG islands in promoters (CGI in promoter), TSSs, 3′UTRs, exons, introns and 5′UTRs against the rank of mRNA-Seq data from the same samples. Cell background color representations are as follows: gray – non-significant association, green - significant association with decreased gene expression, magenta - significant association with increased gene expression (FDR < 0.25 was considered as significant). NA - analysis not available due to missing differentially methylated regions in gene sets. (c) - Venn diagrams showing overlaps between genes and differentially methylated DNA regions used in GSEA. (d) - List of differentially expressed genes (cut-off p < 0.001), in which methylation changes occurred in gene body or promoter regions in each model. Magenta and green arrows indicate increased and decreased levels of mRNA, respectively. Orange and blue arrows indicate increased and decreased methylation events, respectively, which occurred in promoter regions, TSSs, exons, introns, 3′UTRs, 5′UTRs and CGIs (CpG islands).

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