Fig. 3

Artefactual correlations are also driven by mtRNA expression in the Cancer Genome Atlas (TCGA) database. A Heatmap showing median Spearman’s correlation for mtOXPHOS and nuOXPHOS gene expression using TPM normalisation in 31 TCGA cancer types combined (50 samples from each tissue, sampled 100 times). B Violin plot showing total expression from mtDNA-encoded genes in samples from 33 cancer types from TCGA database. C Scatterplot shows median Spearman’s correlation (ρ) of mtOXPHOS-nuOXPHOS gene pairs within 31 TCGA cancer types vs cancer type mean of mtRNA expression as a percentage of total transcripts. Shown for data normalized by TPM, TPM excluding mitochondrial reads for normalising nuclear genes, UQ, MRN and TMM methods. Error bars indicate IQR. Blue line shows linear regression with R² noted within panel. D Scatterplot shows mean over 100 iterations of the cancer type median ρ of mtOXPHOS with 126 random expressed nuclear genes vs cancer type mean of mtRNA expression as a percentage of total transcripts. Shown for data normalized by TPM, TPM excluding mitochondrial reads for normalising nuclear genes, UQ, MRN and TMM methods. 95% confidence interval error bars are smaller than the plotted symbols. The blue line shows linear regression with R² and ρ noted within panel. E Scatterplot shows mean over 100 iterations of the cancer type median ρ within 100 random expressed nuclear genes vs cancer type mean of mtRNA expression as a percentage of total transcripts. Shown for data normalized by TPM, TPM excluding mitochondrial reads for normalising nuclear genes, UQ, MRN and TMM methods. 95% confidence interval error bars are smaller than the plotted symbols. The blue line shows linear regression with R² and ρ noted within panel. Abbreviations for cancer type are given in Additional File 1: Table S5