MLL-r primary samples show global promoter hypermethylation compared with MLL-wt ALLs and normal controls in the HELP assay. Analysis of global methylation differences between the study groups is shown. Hierarchic clustering using a subset of probes, which demonstrated highly significant differences between groups (P < .001), was used to generate heat maps. Heat maps are shown for comparisons between (A) MLL-r ALL versus MLL-wt ALL, (B) MLL-r versus normal controls, and (C) MLL-wt ALL versus normal controls. Individual samples are represented on the heat map as columns, whereas individual probes sets are represented as rows. It is again evident that the groups cluster together and that within each group of samples there are certain probes that are differentially hypermethylated (red) or hypomethylated (blue). (D) Numeric representation of the heat maps shows that for the MLL-r group, there were 1.7- and 2.9-fold more probes, respectively, demonstrating relative hypermethylation than hypomethylation compared with either the other ALL samples or the normal marrow controls. This difference was not evident when MLL-wt ALL samples were compared with normal controls.