Figure 3. Post-translational regulation of co-complex members of aneuploid proteins.

(A) Overall representation of different levels of gene regulation. (B) Number of ubiquitination sites of all, human complex, and top positively and negatively correlated proteins. Wilcoxon test was used to test differences between groups. TF, transcription factors.

Figure 3—figure supplement 1. Expression changes on other chromosomes cannot be fully explained by transcriptional regulation.

Average methylation level of (A) downregulated and (B) upregulated genes in aneuploid vs diploid samples. Wilcoxon test was used to test differences in methylation level of genes between aneuploid and diploid samples (*: p<0.05). (C) The number of targets of differentially abundant transcription factors on aneuploid chromosomes among differentially expressed genes on chromosomes. Expected value and p-value were calculated using a randomization test (*: p<0.05).

Figure 3—figure supplement 2. Transcriptional regulation on expression changes between tumor and normal, and of co-complex members of aneuploid proteins in aneuploid tumors.

(A) Average methylation level of down- and upregulated genes in tumor vs normal samples. (B) The number of targets of differentially expressed transcription factors (TFs) in tumors vs normal among differentially expressed genes. (C) Average methylation level of up- and downregulated co-complex members of aneuploid proteins on other chromosomes in aneuploid vs diploid samples. (D) The number of targets of differentially expressed TFs on aneuploid chromosomes among differentially expressed co-complex members of aneuploid proteins on other chromosomes. Wilcoxon test was used to test differences in methylation levels between sample groups, and expected value and p-value in B and D were calculated using a randomization test (*: p<0.05, n.s: not significant).