Data File S1. Raw genetic interaction dataset.

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 (ε), 7) Adjusted trigenic interaction score (τ), 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

Column description for each of the new supplemental files

1. Query Strain ID
2. Query Allele name
3. Array Strain ID
4. Array Allele name
5. Combined mutant type
   • ‘digenic’ for double mutants resulting from a cross between a single mutant control query and a single mutant array strain
   • ‘trigenic’ for triple mutants resulting from a cross between a double mutant query and a single mutant array strain
6. Raw genetic interaction score (ε)
7. Final genetic interaction score (trigenic τ / digenic ε). Trigenic scores are adjusted according to the τ-SGA model shown in Fig. S4A. Digenic scored receive no further adjustment and the epsilon value is repeated.
8. Interaction p value
9. Query fitness
   • single mutant fitness for single mutant queries
   • double mutant fitness for double mutant queries
10. Array single mutant fitness
11. Combined mutant fitness relative to wild-type.
    • Double mutant fitness for the resulting combined digenic mutants
    • Triple mutant fitness for the resulting combined trigenic mutants
12. Combined mutant fitness standard deviation

Data File S2. Digenic and adjusted trigenic interaction dataset.

This file contains digenic and trigenic interaction scores at an established interaction magnitude cut-off for digenic interactions (p < 0.05, |ε| > 0.08) and trigenic interactions (p < 0.05, τ < -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

Column description for each of the new supplemental files

1. Query Strain ID
2. Query Allele name
3. Array Strain ID
4. Array Allele name
5. Combined mutant type
   • ‘digenic’ for double mutants resulting from a cross between a single mutant control query and a single mutant array strain
   • trigenic’ for triple mutants resulting from a cross between a double mutant query and a single mutant array strain
6. Final genetic interaction score (trigenic tau / digenic epsilon). Trigenic scores are adjusted according to the τ-SGA model shown in Fig. S4A and account for any digenic interactions. Digenic scores receive no further adjustment and the epsilon value is repeated from Additional Table S1.
7. Interaction p value
8. Interaction types:
• Digenic is digenic
• Novel is novel trigenic
• Unclassified apparently novel but with unknown query-query interaction score thus cannot be distinguished from modified and novel
• Modified Q-, Modified Q-A-, Modified Q-A+, Modified Q-A+-, Modified A-, Modified A+ or Modified A-+ are modified trigenic interactions are further broken down by where the overlapping digenic interaction is found: Q- for a negative interaction between query genes, A- for a negative interaction between one or both of the query genes and the array gene, A+ for a positive interaction between one or both of the query genes and the array gene, A+- if both query genes have a digenic interaction with the array but of opposing signs.

Data File S3. Query strains and plasmids list.

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.

Data File S4. Fitness standard for single and double mutant query strains.

This file contains the fitness standard for single and double mutant query strains.

Data File S5. Diagnostic array strain list.

This file contains the complete list of yeast strains present on the diagnostic array, which was used for genetic interaction screens in this study.

Data File S6. MDY2-MTC1 genetic interaction list.

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.

Data File S7. Query bins for trigenic interaction space extrapolation.

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).

1. Gene1 - gene2 double mutant query strain ID
2. Gene1 single mutant control query strain ID
3. Gene2 single mutant control query strain ID
4. ORF1
   • associated with gene1 single mutant control query strain and gene1 of the double mutant query strain
5. ORF2
   • associated with gene2 single mutant control query strain and gene2 of the double mutant query strain
6. Gene1
7. Gene2
8. Allele1
   • associated with gene1 single mutant control query strain and gene1 of the double mutant query strain
9. Allele2
   • associated with gene2 single mutant contro2 query strain and gene1 of the double mutant query strain
10. DigenicInteractionScore
    • digenic interaction score between constitutive single mutants
11. DigenicInteractionScore_bin
    • Bin assignments for digenic interaction score: 1) ε < -0.1; 2) -0.1 ≤ ε < -0.08; 3) -0.08 ≤ ε < 0
12. DigenicInteractionScore_bin_name
    • Name for bin assignments for digenic interaction score: 1) moderately negative digenic interaction score; 2) weakly negative digenic interaction score; 3) very weakly negative digenic interaction score
13. DigenicDegree
    • average digenic interaction degree of constitutive mutants
14. DigenicDegree_bin
    • Bin assignments for digenic degree: 1) 10 ≤ degree < 45 ; 2) 45 ≤ degree < 70; 3) 70 ≤ degree
15. DigenicDegree_bin_name
    • Name for bin assignments for digenic interaction degree: 1) low avg. digenic interaction degree; 2) intermediate avg. digenic interaction degree; 3) high avg. digenic interaction degree
16. AvgProfileSimilarity
    • average digenic interaction profile similarity for constitutive single mutants
17. AvgProfileSimilarity_bin
    • Bin assignments for average digenic interaction profile similarity (r): 1) -0.02 < r < 0.03; 2) 0.03 ≤ r < 0.1; 3) 0.1 ≤ r
18. AvgProfileSimilarity_bin_name
    • Name for bin assignments for average digenic interaction profile similarity: 1) low profile similarity; 2) intermediate profile similarity; 3) high profile similarity
19. TrigenicDegree
    • Number of trigenic interactions per double mutant
20. OverallBin
    • The bin number to which a specified query double mutant was assigned