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Supplementary Information

Treatment Specific Changes in Gene Expression Discriminate in vivo Drug Response in Human Leukemia Cells

B. Clustering of Patients Based on Gene Expression Patterns

Figure 2: "Unsupervised" hierarchical clustering and principal component analysis (PCA).



Figure 2: "Unsupervised" hierarchical clustering and principal component analysis (PCA).

(a) We used 8222 probe sets (fold-change, referred to as "relative change" in the published manuscript) and 8002 (post-treatment) for "unsupervised" hierarchical clustering (all genes after filtering). Post-treatment expression tended to cluster samples by lineage, ploidy and molecular subtypes, whereas this was not the case for the fold-change in gene expression. (b) The top three principal components using all genes on the array, did not discriminate by treatment, based on either post-treatment gene expression or fold-change in gene expression, reflected as distances in three-dimensional-space.