Analysis pipeline used to find CLL-associated differentially methylated regions (DMRs).
CLL cohorts and analysis pipeline used to find CLL-associated differentially methylated regions (DMRs).
Differentially methylated regions in CLL and associated lncRNAs
Identification, validation of differential methylation and expression levels in CLL cohorts. a) The global methylation levels and identification of differentially methylated regions (DMRs) in CLL patient samples. Heatmaps with differentially methylated regions (DMRs, hypermethylated and hypomethylated) in IGHV-mutated and IGHV-unmutated samples over sorted B cells and normal PBMC. The enrichments shown in the heatmap were within a ±3 kb window from differentially methylated region (DMRs). b) The boxplots shows the difference in gene expression levels between IGHV-mutated, IGHV-unmutated, and sorted B cells for same genes obtained using published RNA sequencing dataset (Ferreira PG et al.) and quantitative RT-PCR. The heatmap below each boxplot shows the significance level (p value) of the corresponding gene over B cell (IGHV-M, IGHV-mutated, and IGHV-UM, IGHV-unmutated). c) Kaplan-Meier plots showing the clinical significance of all the validated genes based on high and low methylation levels. The high and low levels were calculated using upper and lower quartile based method for all the genes in total 44 CLL patient samples.