Transcriptome phenotype of CIMP-low and CIMP-high subgroups in the NOPHO ALL2008 cohort. (A) Heat map revealing the relative RNA expression of n = 213 DEG between CIMP-low (n = 43) and CIMP-high (n = 65) T-ALL samples; genes hierarchical clustering highlights a cluster 1 with higher expression in CIMP low (134 genes) and a cluster 2 with higher expression in CIMP high (79 genes). (B,C) Heat maps presenting the mean β-values of CpGs located on the promoter region (B) or on the gene body (C) of the DEG visualized in the same gene and sample order as in panel A. (D) Pearson correlation between clusters 1 and 2 gene RNA expression and their mean promoter region DNA methylation. (E) GO analysis of DEGs with higher expression in CIMP low (n = 134 genes, cluster 1) and CIMP high (n = 79 genes, cluster 2), respectively. (F) Volcano plot with highlighted n = 213 DEG in n = 108 T-ALL. (G) RNA expression (in VST counts) heat map using hierarchical clustering of 108 T-ALL samples, revealing 40 selected genes relevant in T-ALL biology or differentially expressed between CIMP-low and CIMP-high subgroups. Sorted CD34⁺ and CD3⁺ T cells and lymph node are illustrated as normal cell types in the heat maps. DEG, differentially expressed gene; GO, gene ontology.