Figure 2.

The average expression of genes carrying a mutation is similar to those in samples without the mutation, but aggregated expression of mutated genes is lower. (A) The expression level (as measured by log FPKM) of genes in the mutant sample was plotted against the average expression of the same gene in samples not harboring the mutation. The Spearman correlation is 0.92. Due to the limited sample size and limited number of samples carrying a mutated copy of a given gene, we do not have strong evidence to demonstrate lower expression of mutated genes on an individual gene basis. (B) The distribution of expression (log FPKM) for all mutated genes aggregated together is plotted with the expression of the unmutated versions of these genes in other samples. We find slightly lower expression within the mutant gene group (permutation P = .032). Such aggregation of the data helps to overcome the per-gene sample size limitation mentioned previously.