Figure 3 | Scientific Reports

Figure 3

From: Alpha-oxoglutarate inhibits the proliferation of immortalized normal bladder epithelial cells via an epigenetic switch involving ARID1A

Figure 3

Reprogrammed DNA methylation architecture by α-OG treatment. (A) QC (density plots) of probes for DNA methylation levels (β-values). The orange group represents untreated samples, which show a slight hypermethylation pattern. The green group, α-OG-treated samples, shows a more even distribution of beta values across probes. (B) Density Bean Plot of probes for β-values in two experimental samples. Distribution of β-values across each sample (orange, untreated; green, α-OG-treated) was shown. (C) Volcano Plots indicates differentially methylated probes between untreated and treated samples. Each dot represents a single CpG probe on the array, with hypomethylated probes colored blue and hypermethylated probes colored orange. The upper plot defines differential methylation based on statistical significance alone (Group A – hypomethylated probes: p < 0.0005, Group B – hypermethylated probes: p < 0.0005). The lower plot shows the exact same volcano plot, but defines differential methylation based on both statistical significance and β-value difference (Group C - hypermethylated probes: p < 0.05 and β-value difference > 0.1, Group D - hypomethylated probes: p < 0.05 and β-value difference > 0.1). (D) Sample-specific β-values are shown as heatmaps for the probes in Groups A-D. Group A: 873 probes, Group B: 382 probes, Group C: 32 probes, Group D: 366 probes.

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