Fig. 4

Hierarchical clustering of CGIDs associated with DM lncRNAs. a PCA of CpGs associated with lncRNAs on SWAN normalized β values on 82 BCP-ALL samples obtained from DNA methylation array. Each point represents a BCP-ALL sample. DUX4, Ph-like, NH-HeH, LH, and others are represented by orange, rose, blue, green, and gray, respectively. b The heatmap representing hierarchal clustering on 544 differentially methylated (DM) CGIDs associated with 434 lncRNAs in DUX4 subtype. In the DUX4 subtype, we identified 328 (76%) differentially hypo-methylated and 106 (25%) hyper-methylated lncRNAs. c The heatmap representing hierarchal clustering on 518 DM CGIDs associated with 450 lncRNAs in the Ph-like subtype. In Ph-like subtype, we observed 302 (67%) hyper-methylated lncRNAs and 148 (33%) hypo-methylated lncRNAs. d The heatmap representing hierarchal clustering on 295 DM CGIDs associated with 234 lncRNAs in NH-HeH subtype. In the NH-HeH subtype, we identified 200 (86%) hypo-methylated and 34 (14%) hyper-methylated lncRNAs. The heatmap is plotted using SWAN normalized beta values. The barplots below each heatmap represent the distribution of DM lncRNAs in the genome (promoter-TSS and gene body) lncRNAs from each subtype. The distribution DM promoter-TSS lncRNAs are as follows: 25%, 29%, and 39% in DUX4, Ph-like, and NH-HeH subtype, respectively