To systematically explore complex genetic interactions, we constructed ~200,000 yeast triple mutants and scored negative trigenic interactions. We selected double-mutant query genes across a broad spectrum of biological processes, spanning a range of quantitative features of the global digenic interaction network and tested for a genetic interaction with a third mutation. Trigenic interactions often occurred among functionally related genes, and essential genes were hubs on the trigenic network. Despite their functional enrichment, trigenic interactions tended to link genes in distant bioprocesses and displayed a weaker magnitude than digenic interactions. We estimate that the global trigenic interaction network is ~100 times as large as the global digenic network, highlighting the potential for complex genetic interactions to affect the biology of inheritance, including the genotype-to-phenotype relationship.
AdditionalDataS1
This file contains digenic interaction scores as well as raw and adjusted trigenic interaction scores in a tab-delimited format with 12 columns: 1) Query Strain ID, 2) Query allele name, 3) Array strain ID, 4) Array allele name, 5) Combined mutant type, 6) Raw genetic interaction score (epsilon), 7) Adjusted trigenic interaction score (tau), 8) p-value, 9) Query fitness, 10) Array single mutant fitness, 11) Combined mutant fitness relative to wild-type, 12) Combined mutant fitness standard deviation
AdditionalDataS2
This file contains digenic and trigenic interaction scores at an established interaction magnitude cut-off for digenic interactions (p < 0.05, || > 0.08) and trigenic interactions (p < 0.05, < -0.08) in a tab-delimited format with 8 columns: 1) Query Strain ID, 2) Query allele name, 3) Array strain ID, 4) Array allele name, 5) Combined mutant type, 6) Final genetic interaction score (tau), 7) p-value, 8) Interaction type
AdditionalDataS3
This file contains the complete list of yeast strains and plasmids that were used in this study. The ‘Strain Pairing List’ tab lists the double mutants and their corresponding single mutant control strains that were used to generate trigenic interaction scores. The ‘Genotypes’ tab lists the complete genotype of each strain including control strains that were used to derive the fitness standard. The ‘Plasmids’ tab lists that plasmids that were used in this study.
AdditionalDataS4
This file contains the fitness standard for single and double mutant query strains.
AdditionalDataS5
This file contains the complete list of yeast strains present on the diagnostic array, which was used for genetic interaction screens in this study.
AdditionalDataS6
This file contains the trigenic interactions list of MDY2-MTC1 and digenic interaction list of MDY2 and MTC1 corresponding to Fig. 3. The ‘Tetrad Analysis’ tab contains confirmations results obtained from tetrad analysis: SS is synthetic sick, SL is synthetic lethal. The ‘Genetic interactions’ tab contains columns that are annotated with ‘CellMap’ since they contain genetic interactions from (7) downloaded from theCellMap.org (26) as well as scores derived in this study.
AdditionalDataS7
This file contains a list of queries used for trigenic interaction space extrapolation. The digenic interaction parameters used for binning for each double mutant query and its single mutant counterparts was derived from the global digenic interaction network (7).
