Fig. 4

Validation of differential methylation and expression levels in CLL cohorts. a Boxplots on top shows the difference in distribution and level of methylation between IGHV-mutated, IGHV-unmutated, and sorted B cells for two selected genes (CRNDE and AC012065.7) obtained using pyrosequencing. 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. d Gene expression levels of CRNDE using increasing concentrations of DAC treatment in different leukemic cell lines. e The illustrations (left panel) represents the protein coding genes IRX5 and GDF7 within 10-kb proximity of selected lncRNAs CRNDE and AC012065.7, respectively. The expression values for these lncRNAs and nearby protein coding genes are presented in right panel of the figure. The values in the panel represents log2-fold change in comparison between normal B cell and CLL groups (96 patients cohort, 55 IGHV-mutated, and 41 IGHV-unmutated), positive values means expression is more in CLL groups and vice versa