Hierarchical clustering of the leukemias and their mutated genes based on common insertion sites. A matrix of 71 leukemias against the 102 CIS genes identified by analysis of transposon insertions by the GKC method was constructed. Although 73 leukemias were subjected to ligation-mediated PCR, sample 120992 did not have any insertions that were mapped and sample 138641 had only 44 insertions sites that were mapped, but none of these contributed to any CISs; thus, these 2 samples do not appear in the heatmap because the heatmap is based on the co-occurrence of insertions in CISs. Hierarchical clustering was performed on a binarized version of the matrix using the Hamming distance metric along both the rows and columns, to aggregate leukemias and CIS genes with similar insertions patterns. The 2 resulting dendrograms were visualized as a heatmap, where black squares indicate the presence of at least one insertion in the tumor, and gray no insertion site. Leukemia rows highlighted in red indicate a BCP-ALL phenotype (n = 15; only 14 rows highlighted in red because no insertions were found in the called CIS for sample 138895). The clustering and visualization were performed using the R programming language (Version 2.10.0; http://www.r-project.org) and Bioconductor (Version 2.5; http://www.bioconductor.org).