Figure 3.

The Global Effects of Genomic Alterations on Protein and mRNA Abundances

(A) Volcano plot summarizing the effect of missense mutations on the respective protein abundances (ANOVA test). Hits at permutation-based FDR < 0.1 are colored.

(B) Volcano plot summarizing the effect of LoF mutations on the respective protein abundances (ANOVA test). Hits at permutation-based FDR < 0.1 are colored.

(C) STRING network of the proteins downregulated by LoF mutations at FDR < 0.1.

(D) Boxplots illustrating the protein abundance differences between all proteins and proteins with heterozygous or homozygous LoF mutations.

(E) Volcano plot summarizing the effect of LoF mutations with both mRNA and protein measurements on the respective mRNA abundances (ANOVA test). Hits at permutation-based FDR < 0.1 are colored.

(F) Venn diagram displaying the overlap between proteins and mRNAs affected by LoF mutations. Selected unique and overlapping proteins are displayed.

(G) Volcano plot summarizing the effect of recurrent copy number alterations on the protein abundances of the contained genes (binary data; ANOVA test). Red and blue points highlight genes with amplifications and losses, respectively. Enlarged points highlight genes at permutation-based FDR < 0.1.

(H) Bar plot illustrating the number of affected proteins by CNAs per genomic locus.

See also Figure S5.