Figure 1
From: Mitochondrial-nuclear epistasis underlying phenotypic variation in breast cancer pathology
Significant mito-nuclear interactions. (a) Shown is a heat map of -log10 p-values ordered by mitochondrial genome position on the y-axis and nuclear genome position (chromosome, position) on the x-axis. All p-values shown meet the FDR q-value threshold for statistical significance of < 0.05 and Bonferroni p-value < 0.05. The Heatmap was produced in R using ComplexHeatmap. (b) Genomic targets of nuSNPs. Syn: synonymous substitution, UTR: untranslated region. (c) Circos plot of the mitochondrial genome (chrM) with genes color coded and labeled and tRNAs denoted as yellow bands. Points outside of the genome represent the variant allele frequency (VAF) of the mtSNPs. Red circle: VAF < 0.1, Blue circle: 0.1 ≥ VAF < 0.2, Orange circle: 0.2 ≥ VAF < 0.3, Green square: VAF ≥ 0.3. (d) Genomic information for the interacting SNPs significant in TCGA and METABRIC cohorts. The p-value and false discovery rate (FDR) q-value are from the TCGA data analysis. (e) Boxplot of TCGA log2 mean size area normalized by number of nuclei (y-axis) for the nuSNP rs17320521 (WSCD2) by mtSNP rs869096886 (MT-ND4) interaction. The x-axis is the genotypes for the nuSNP by mtSNP allele pairs. (f) Same as (e) except for METABRIC data.
