Structure of genetic interactions within and between mitochondria and the secretory pathway. (A) A heat map of log10 P-values for the enrichment of synthetic genetic interactions (S-score < −3) between genes annotated as functioning in different pathways of the secretory system, mitochondria, or related pathways. Genes were manually assigned a single annotation based on curation of the literature (Table S2). Enrichment P-values were calculated using the binomial distribution as the probability of observing as many or more synthetic interactions between genes with the indicated annotations, given the number of measurements and an expected probability of synthetic interaction that accounts for the overall interaction frequency for each annotation (see Materials and methods for more details). Enrichment P-values were calculated after accounting for the overall frequency of interactions for each annotation. (B) A heat map of enrichments of synthetic interactions (as in A) for the different major branches of the cellular lipid biosynthesis machinery. (C) Genetic connection scatter plot for the average of ERMES component genes MDM10, MDM12, MDM34, and MMM1. The x axis represents the cosine correlation between the mean of ERMES genes interaction scores, and the y axis indicates the mean interaction score between the ERMES genes and each gene in the MITO-MAP. Every point in the scatter plot represents one gene. The cosine correlation values for points corresponding to the selected genes themselves were computed using the mean of the interaction score vectors for the remaining selected genes. In cases where the genetic interaction score was not measured, the point is plotted in gray along the line y = 0.
