Figure 6.

Acquisition of the aneuploidy-specific profile reshapes gene expression and correlates with increasing c-Myc expression in human cancers. (A) Heat map showing genes from the indicated chromosomes whose expression (RNA) significantly correlated with the similarity index (similarity to the DNA copy number profile as determined by GISTIC from Fig. 4) of terminal tumors from the indicated PRG5 and Mad2 mice. Gene names are color-coded according to chromosome numbers and are sorted from top left to bottom right. See Supplemental Table S5 for a list of genes. (B) Enrichment of the CIN-induced gene expression profile (as shown in A and in Supplemental Table S5) in TCGA tumor cohorts gene lists of significantly up-regulated genes relative to their nontumor controls. (C) Enrichment of the CIN-induced gene expression profile (as shown in A and in Supplemental Table S5) in TCGA cohorts in correlation with MYC expression. A Spearman correlation coefficient between the gene's expression and MYC expression (among all samples) and the posterior probability that the gene is correlated with MYC was calculated. The ranked gene lists were then tested for enrichment with Bioconductor fgsea on the CIN-induced gene expression profile (Supplemental Table S5).