Expression profiling of 12 methotrexate resistant colonies with amplification of DHFR*. (a) Unsupervised hierarchical clustering (Pearson) of genes with variable expression across the data set (SD ≥ 0.3) and present in >75% of samples (3,931 genes). Methotrexate resistant colonies represent four different integration sites, indicated by the shaded boxes below the dendrogram. (b) Comparison of expression of MYC target genes in the two clusters. The median absolute log2 ratio change in expression of MYC target genes in the right cluster compared to the left cluster is significantly higher than a similar comparison using 1,000 sets of 380 randomly selected genes (p = 2.2e-16).