AML signature gene expression changes in the MLL-AF9 AMLs. (A) Heatmap displays gene expression profiles of MLL-AF9 rearranged cultured cells and their derived leukemic bone marrow cells. Unbiased hierarchical cluster analysis is shown for 7 primary (AML) and 2 secondary (2nd AML) leukemias compared with 2 cultured cell lines used for injection (S1, sample 1; S2, sample 2). (B) Gene set enrichment analysis plots show that genes upregulated in human LSCs were enriched in the AMLs (left, normalized enrichment score = −1.84, false discovery rate q value = 0) whereas genes downregulated in LSCs were enriched in the injected cells (right, normalized enrichment score = 1.33, false discovery rate q value <0.074).