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. Author manuscript; available in PMC: 2020 Aug 11.
Published in final edited form as: Cell. 2019 Oct 31;179(4):964–983.e31. doi: 10.1016/j.cell.2019.10.007

Figure 2. Impact of Copy Number Variation (CNV) on Protein Abundance.

Figure 2.

(A) DNA variations (CNV baf, B-allele frequencies; CNV Ir, adjusted log coverage ratios; DNA methylation) with cascading cis-association (associations with all types of mRNA, global protein, and phosphopeptide abundances), overlapped with phosphopeptides significantly differentiated by clinical features (tumor versus NAT and tumor grade). Genes in bold are associated with CNV events involving chromosome 5 or 7 gain and 14 loss.

(B) The cis and trans associations of chromosome arms (3p, 5q, 7p, 9p, and 14q) and CpG island methylator phenotype (CIMP). Significant (adjusted p < 0.1) positive (red) and negative (blue) associations for individual chromosomes (left), summed associations (middle), and corresponding enriched upregulated (red) and downregulated (blue) pathways (adjusted p < 0.05) are annotated (right).

See also Figure S2 and Table S3.