Figure 2
From: Mitochondrial-nuclear epistasis underlying phenotypic variation in breast cancer pathology
Biological impact of the significant mito-nuclear interaction. (a) Hematoxylin stain channel of image tile #28943 at 40X magnification from subject TCGA-AR-A5QQ with genotype: GG_AA for rs17320521 by rs869096886. (b) Hematoxylin stain channel of image tile #6545 at 40X magnification from subject TCGA-EW-A1PB with genotype: AA_GG for rs17320521 by rs869096886. (c) Histograms of log2 size area of the nuclei in the images from subject TCGA-AR-A5QQ with genotype: GG_AA for rs17320521 by rs869096886 and subject TCGA-EW-A1PB with genotype: AA_GG for rs17320521 by rs869096886. The x-axis is log2 size area and the y-axis is the density of the data. (d) Same as Fig. 1e except for TCGA WSCD2 gene log2 (RSEM + 1) on the y-axis and 284 of the 286 patients. p-values for the comparisons are from Mann–Whitney tests with the hypothesis that the median WSCD2 gene expression of the patients with genotype homozygous for the minor alleles is the same as the other genotypes and the alternative is that the median is less. The dotted line is the median expression of WSCD2 in TCGA normal patients. (e) Table with median values of WSCD2 gene log2 (RSEM + 1) for sample groups. (f) t-test comparisons of RNA-Seq FPKM gene expression data between TCGA patients with genotype homozygous for the minor alleles for of rs17320521 by rs869096886 versus all other genotypes. For each comparison, the number of differentially expressed genes (DEGs) is shown based on a false discovery rate < 0.05 and fold change >|1.5|. (g) Interaction networks derived from the 16 genes from the overlap of the DEGs in (f), WSCD2 and MT-ND4 using the Ingenuity Pathway Analysis Knowledge Base content version 62,089,861. These focus genes are shaded gray. Square: cytokine, diamond: enzyme, triangle: kinase, horizontal oval: transcription regulator, horizontal rectangle: ligand-dependent nuclear receptor, double circle: complex, single circle: other. (h) Same as (g). except the interaction networks derived from the 9 of the 16 genes from the overlap of the DEGs in (f), WSCD2 and MT-ND4. Vertical rectangle: G-protein coupled receptor, vertical oval: transmembrane receptor, hexagon: translation regulator.
