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. 2022 Dec 5;13:7494. doi: 10.1038/s41467-022-34460-w

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© The Author(s) 2022

Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — a Arm-level SCNA events. Red denotes amplification and blue denotes deletion. Significant events are highlighted using red and blue (q < 0.10). b Focal SCNA events. Focal peaks with significant copy number amplifications (red) and deletions (blue) (q < 0.05) are shown. c Cox regression analysis of significant arm-level CNA and focal CNA events. d Identifying cis- and trans-effect of 3p deletion. Proteins are ranked based on the correlation between protein abundance and 3p CN. e Trans-effect of 3p deletion on ULK1 S469 phosphorylation level. Boxplots show the median (central line), the 25–75% IQR (box limits), the ±1.5 × IQR (whiskers). P value is derived from two-sided Wilcoxon rank-sum test. f Correlations between ATG7 protein abundance and MHC molecules. g Cis and trans- effects of CTNNB1 deletion on cadherin-catenin complex abundances. Cox regression analysis of cadherin-catenin complex abundances are shown in left. h A model depicting the association of 3p deletion and poor prognosis in tRCC.