(A) Box and whiskers plot of whole chromosome gain-loss events in tumors, scored by averaging the log2 ratio of aCGH fluorescence from tumor over normal (aCGH ratio) for each chromosome with a ±0.3 cut-off. Line – median, Box – interquartile range, Whisker – range. (B) Box and whiskers plot of the aCGH ratio for each chromosome. Two-way ANOVA, Bonferroni post-test **p<0.01, ***p<0.001 (C) Scatter plot showing average chromosome aCGH ratio of HCC and thymus tumors. Gain of Chr15 (red), loss of Chr13 (green), and tissue specific gain or loss of Chr4, Chr12, and Chr18 (blue). (D, E) Scatter plots of average chromosome aCGH ratio plotted against average mRNA ratio for (D) HCC and (E) T-ALL. r is the Pearson Correlation with indicated P value. (F, G) Expression analysis of genes on chromosome 15 (F) and chromosome 18 (G) comparing HCC and T-ALL samples. (H) Scatter plot showing chromosome normalized aCGH ratio for every gene in HCC and T-ALL. The three listed genes are likely hybridization artifacts due to a mixed 129/C57BL6 background. (I, J) Number of focally amplified or deleted regions per tumor (I) and the number of genes amplified or deleted per tumor (J) scored with ±0.3 cut-off for the chromosome normalized aCGH ratio. *p<0.05, **p<0.01, Mann-Whitney Test comparing T-ALL and HCC.