Fig. 6
Identification of DNA methylation changes following oncogenic KrasG12D induction using RRBS. a Venn diagram of unique and overlapping differentially methylated cytosines (DMCs) for 12, 24, and 48 hrs. DMCs were classified based on p value < 0.01 and methylation difference > |10%|. b Methylation ratio of DMCs normalized to the Z scale and plotted for 0, 12, 24, and 48 hrs. Yellow: hypermethylated DMC. Blue: hypomethylated DMC. Black: no change. c Annotation of DMCs with CpG islands and shores. d Annotation of DMCs with genic features. e Pathway enrichment analysis of DMCs located within ± 3 kb of gene transcription start sites (TSSs) for 12, 24, and 48 hrs using the MSigDB hallmark gene set collection. Color scale: −log10(FDR). f Protein-protein interaction network obtained from DMCs for the epithelial to mesenchymal transition (EMT) pathway using the STRING database. Confidence score: 700. g Distribution of DMCs within various repetitive element types. h Methylation ratio of DMCs distributed within non-repeats and repetitive elements. Non-repeat n = 10,864, LINE n = 1411, LTR n = 791, Simple repeat n = 465, SINE n = 347. Wilcoxon signed rank test was used to test for differences between 0 and 24 hrs for each category. * significant at p value < 0.05