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. 2024 May 22;630(8015):149–157. doi: 10.1038/s41586-024-07442-9

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© The Author(s) 2024

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 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/.

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Extended Data Fig. 5 — a, GSEA of median log2 protein expression ratios (strain/euploid) of genes encoded on euploid chromosomes across all disomic strains. Statistically significant enrichment scores (FDR < 0.05) are coloured in purple (protein). b, Median relative expression of UPS components on euploid chromosomes in aneuploid natural S. cerevisiae isolates. The adjusted p-values (Benjamini–Hochberg-corrected) of one-sample, two-sided t-tests comparing the mean of each group to the expected mean expression of UPS components in euploid isolates (µ = 0) are shown above the box plots (core particle: p = 0.000053; RP base: p = 0.044; ns: p > 0.05). In box plots, the centre marks the median, hinges mark the 25th and 75th percentiles and whiskers show all values that, at maximum, fall within 1.5 times the interquartile range. c, Components of the UPS and their regulation in aneuploid isolates (trans expression). Volcano plots show the results of one-sample, two-sided t-tests comparing the mean log2 protein ratios of proteins expressed on euploid chromosomes of 95 aneuploid isolates to μ = 0. Proteins with statistically significant differential expression after multiple hypothesis correction (Benjamini–Hochberg) are coloured in dark grey. Components of the UPS are highlighted and labelled as blue dots in separate panels. d, Volcano plots showing results of one-sample, two-sided t-tests as in Fig. 4c, but for all diploid natural isolates (n = 73, left panel), or all isolates but diploid isolates (n = 22, right panel). e, Volcano plots as in Fig. 4c, but with the x and y axes scaled to match.