Mapping Gene Associations in Human Mitochondria using Clinical Disease Phenotypes
(A) For each gene (black dots), the average QPA (y-axis) to all other genes within a functional module was calculated. Red lines represent the median (50th percentile) of all QPA averages within a module. Boxes indicate the 25th and 75th quartiles, with minimum and maximum data points as lines that extend from each end of the box. The grand mean of all modules (blue line) is the QPA average across all gene pairs of all nine modules, which was significantly higher than for pairs outside modules (orange line). (B) Module gene relationships are predicted through functional (LR) and phenotypic (QPA) associations showing the usefulness of phenotype similarity scores in disease gene network analysis. The edge colors are: Red – gene pairs with highest correlation of QPA and LR; blue – gene pairs with lower QPA-LR correlation; orange and light blue – gene pairs with QPA only at higher (> = 0.4) and lower confidence (<0.4), respectively (see Table S4 for data). Diseases caused by the six genes labeled “*” are known to respond to vitamin treatments (riboflavin, thiamine, and pyridoxine). Abbreviations: AKDH, Alpha ketoglutarate dehydrogenase; BCKDH, Branched chain alpha keto acid dehydrogenase; GCC, Glycine cleavage system; PDH, Pyruvate dehydrogenase; RCC, Respiratory chain complex; TCA, Tricarboxylic acid cycle; UC, Urea cycle.