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. 2022 May 16;11:e75526. doi: 10.7554/eLife.75526

Figure 1. Transcriptomic and proteomic changes in aneuploid tumors.

(A) Data used in this study and schematic representation of the performed analyses. (B) Cancer-type-specific, whole-chromosome-level alterations across 32 cancer types. The color encodes the degree of their enrichment (standard residuals of the chi-square test multiplied by the alteration score [–1 in the case of deletion and 1 in the case of amplifications]). (C) Average percentage of differentially expressed genes or abundant proteins on aneuploid and other, non-aneuploid chromosomes (among the detected genes on the respective chromosomes).

Figure 1.

Figure 1—figure supplement 1. Proteome data coverage and differential expression changes on other chromosomes.

Figure 1—figure supplement 1.

(A) The number of genes covered by transcriptomic and proteomic data for The Cancer Genome Atlas cancer patients comprising colorectal adenocarcinoma (COREAD), breast (BRCA), and ovarian (OV) cancer types. (B) Average percentage of differentially expressed genes on co-amplified and non-co-amplified chromosomes across 60 whole-chromosome-level amplifications. Paired Wilcoxon test was used to test differences between the groups. (C) Average percentage of differentially expressed genes on the aneuploid chromosome and other, non-aneuploid chromosomes (left), and percentages of differentially expressed genes on other chromosomes (right) in thyroid cancer (THCA) chromosome 7 amplification. Percentage was calculated as the ratio of differentially expressed genes from each chromosome to the total number of expressed genes on that chromosome. Red bars show the percentage for chromosome 5, 16, and 20 which are strongly co-amplified with chromosome 7 in THCA.