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. 2022 Jun 3;15:76. doi: 10.1186/s13045-022-01291-7

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© The Author(s) 2022

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 2 — Effects of copy number alterations on mRNA and protein abundance. A Functional effects of CNAs on mRNA and proteins. Top panels: correlation of CNA to mRNA and protein abundance. Positive and negative correlations are indicated in red and blue, respectively. Genes were ordered by chromosomal location on the x and y axes. Diagonal lines indicate cis-effects of CNA on mRNA or proteins. Bottom panels: number of mRNAs or proteins that were significantly associated with a specific CNA. Gray bars indicate correlations specific to mRNA or proteins, and black bars indicate correlations with both mRNA and proteins. B Venn diagrams depicting the cascading effects of CNAs. It shows the overlap between significant cis events across the transcriptome, proteome, and phosphoproteome. C Pathways enriched for 139 significant cis-effect genes. D Venn diagram shows the significant cis events restricted to cancer-associated genes (CAGs) across multiple data types. E Cis- and trans-effects of 10 significant cis-effect CAGs. Affected proteins are grouped by pathway. F Arm-level CNAs. Red denotes amplification and blue denotes deletion. G Chromosomal alterations associated with prognosis (overall survival). Volcano plot showing log2-based hazard ratio for each alterative chromosome. H Overall survival analysis of patients with 5p or 7q gain versus WT (p value from log-rank test). I Volcano plot showing log2-based hazard ratio (overall survival) for significant positive cis-effect genes on chromosomes 5p and 7q, respectively. The dots represent proteins, and the triangles represent mRNA. J Overall survival analyses of BLCA TCGA patients with high or low levels of SND1 mRNA abundance (p value from log-rank test). K Volcano plot showing the correlation between enriched KEGG pathways scores (sample-specific gene set enrichment analysis (ssGSEA)) and SND1 protein abundance. L Volcano plot showing the correlation of transcription factors (TFs) with SND1 based on protein level. TF, highlighted in red, reportedly interacts with SND1. M Heatmap of SND1 protein abundance and trans-effect cell-cycle-related proteins. N Correlation of STAT3 activity with the cell cycle enrichment score by ssGSEA. O Correlation of STAT3 with the cell cycle enrichment score by ssGSEA in TCGA cohort. P Heatmap of STAT3 activity change and the target genes of STAT3 that participated in cell cycle. Confidence intervals (95%) of hazard ratio coefficients (overall survival) for each gene mRNA expression level were based on multivariate Cox regression models (tumor samples, n = 42). Q Volcano plot showing the correlation of kinase with STAT3 based on protein level. The kinase highlighted in red has been reported to be a STAT3 kinase. R Correlation and heatmap of CDK5 protein abundance with STAT3 phosphorylation change. S A model depicting the gain of chromosome 7q. The p values in K–R were calculated by Spearman's correlation test