Supervised clustering of genes differentially expressed among major sample groups. (A) This hierarchical classification was performed using 469 probe sets detecting differential expression among sample groups (Figure 2A). Samples were preclassified according to oncogenic group assignment as defined in Figure 2B. The same conventions for sample annotations are used. The HOXA_R subgroup is indicated (HOXA-rearranged, n = 4, and HOXA-related, n = 2). Clusters of genes defined by this supervised clustering are indicated (clusters 0-12). Genes of particular interest are labeled using Locuslink symbol, and genes without significant thymic expression are highlighted in yellow (ectopic thymic expression). The cluster C9, which is defined by HOXA-expressing samples and contains HOXA genes, is highlighted in red. (B) List of genes from clusters C8 and C9 and relative expression in oncogenic subgroups. Genes from cluster C8 are frequently highly expressed in subsets from the HOX_R group; cluster C9 is defined mainly by the HOXA-expressing samples (HOXA_R, CALM-AF10, and MLL) and includes HOXA genes (in red); “ectopic” genes with respect to thymus expression are highlighted in yellow. NA indicates Locuslink symbol not available. Relative expression in each T-ALL group is shown by color scale.