Hierarchical clustering of DNA methylation profiles.

<p>A) Unsupervised Euclidean hierarchical clustering was performed using beta values for the 1347 most variable CpG sites in T-ALL (standard deviation ≥0.30). In the dendogram each individual is represented as a vertical row and the specific CpG sites are shown in the horizontal columns. High methylation levels are shown in red and low levels in green, according to the Beta value scale bar in the figure where 1.0 is fully methylated and 0 is unmethylated. The T-ALL methylation subtypes are marked in the figure as low, intermediate and high, and with the merged classification in CIMP− and CIMP+ cases. The methylation status of the 1347 CpG sites of normal bone marrow samples (N1–N3) and two stimulated primary T-cell lines (P7/R2 and L2) are shown next to the hierarchical cluster. B−D) The mean CpG methylation levels within and outside CpG islands were examined. The distribution of mean methylation levels in low (n = 22), intermediate (n = 6) and high (n = 15) methylation subtypes are shown for: B) the entire array (26436 sites), C) within CpG islands (19211 sites), D) outside CpG islands (7225 sites). The significance (independent samples t-test) for differences in methylation between groups is shown.