Fig. 4

DNA methylation analysis and integration of omics layers. A Schematic workflow. B Number of hypermethylated (dark) and hypomethylated (light) positions in remission (green) and non-remission (blue) patients at each time point after therapy induction obtained from the pairwise analysis of the discovery cohort. Negative numbers are used to show the number of hypomethylated positions. C Venn diagram showing the number of DMPs in remission and non-remission patients. D Heatmap of DMPs, which are correlated with DEGs, showing scaled mean methylation intensities at each time point in remission and non-remission samples. E Heatmap showing significant enrichment, quantified by odds ratio, of transcription factor binding sites (TFBS) in DMPs that are correlated with DEGs. Selected top TFs are visualized. F Over-representation and under-representation of DNAm-linked DEGs in co-expression modules. The over-/under-representation is quantified as the ratio of the observed and expected number of correlated genes present in each module under the chi-square distribution. G GO terms enriched in DNAm-linked co-expression modules. Dot size is proportional to the gene ratio and color corresponds to the p-value of enrichment