Protein complex and protein abundance buffering analysis. (A) Networks connecting proteins that are annotated as components of stable protein complexes by either CORUM or REACTOME databases. The source nodes (red dots) in the networks are proteins that are encoded on chromosome 12 and are upregulated in trisomy 12 CLL at both protein and RNA levels. The target nodes (blue triangles) are proteins that are encoded elsewhere and are upregulated in trisomy 12 CLL. (B-C) The shape of the edges indicates whether the target nodes are upregulated at RNA level (solid lines) or not (dotted lines). Normalized expression levels for chromosome 12 proteins/RNAs in trisomy 12 CLL (B) and chromosome 19 proteins/RNAs in trisomy 19 CLL (C) compared with diploid patient samples. Dosage effects of copy-number variants are seen both for protein and RNA expression and are more pronounced for RNA. (D) Classification of differentially expressed genes (trisomy 12 vs diploidy 12) on chromosome 12 and differentially expressed genes (trisomy 19 vs diploidy 19) on chromosome 19 into buffered (defined in main text), nonbuffered, enhanced, and undetermined groups. (E) Gene set enrichment analysis (Fisher’s exact test) for proteins in the nonbuffered group of trisomy 12 CLL. (F) Comparison of cis-effects of trisomy 12 at RNA and protein levels. The y axis shows the difference between log₂(RNA fold change) and log2(protein fold change) for genes on chromosome 12. The comparison is stratified by whether a protein is annotated as a member of a stable complex in the CORUM or REACTOME database. The error bar indicates 1 standard deviation around the mean. (G) Empirical cumulative distribution function curves of copy-number variant mRNA (dashed lines) and copy-number variant protein (solid lines) expression correlations for genes on chromosome 12 (magenta) and chromosome 19 (blue).