Change in RNA and protein expression upon chromosome arm gain or loss. (A) Heatmaps displaying the difference in RNA expression (top) or protein expression (bottom) between cell lines with a chromosome arm gain (left) or chromosome arm loss (right) compared with cell lines with neutral ploidy for that arm. The mean RNA or protein expression differences per chromosome arm are displayed. (B) Heatmaps displaying the same analysis as in A, but only for each aneuploid chromosome. (C) Volcano plots displaying the difference in RNA expression (top) and protein expression (bottom) versus the P-value, per gene, between cells with Chromosome 5q gain (left) and cells with Chromosome 5q loss (right) compared with cell lines with neutral ploidy for Chromosome 5q. Genes encoded on Chromosome 5q are indicated in red (upon gain) or blue (upon loss), and all other genes are indicated in black. (D) Heatmap of the DNA ratio, RNA expression difference, and protein expression difference, per chromosome arm, in MCF-7 cells relative to cells neutral for each chromosome arm (top). Scatterplots showing the relationship between the DNA ratio and the RNA or protein expression differences (bottom). Linear regression with 95% confidence intervals is plotted against the data.
