Supplemental Files

File S1. Conditions, strains and single mutant fitness.

1.3MB

This file contains multiple tabs:

Query genes
Lists the 26 nonessential deletion and essential TS alleles screened as query mutant strains in this study.
Conditions
Lists the 15 conditions tested in this study.
Mutant Fitness_Reference
Lists single mutant fitness in the reference condition for all strains represented on the nonessential deletion (DMA) and essential TS (TSA) mutant arrays. Fitness estimates are based on normalized colony size measured after 3 or 5 days of incubation at 26oC.
Condition Responsive Genes
Lists genes that exhibit a significant differential positive fitness score in at least 2 conditions and/or a significant differential negative fitness score in at least 4 conditions.
Mutant Fitness_Conditions
Lists single mutant fitness of all strains represented on the nonessential deletion (DMA) and essential TS (TSA) mutant arrays in each of the 14 test conditions.
Diff. Mutant Fitness_Conditions
Lists differential mutant fitness of all strains represented on the nonessential deletion (DMA) and essential TS (TSA) mutant arrays in each of the 14 test conditions.

Mutant Fitness_Conditions and Diff. Mutant Fitness_Conditions datasets are provided in tab-delimited format with 19 columns:

  • Systematic Name
  • Gene Name
  • Allele (Essential genes only)
  • Strain ID
  • On Diagnostic Array
  • Fitness or Differential fitness measurements in the indicated condition (Columns 6–19)

File S2. Functional enrichment: Single mutant fitness and differential fitness.

0.5MB

This file contains multiple tabs:

GSEA
Lists GO Biological Process terms enriched among mutants with differential negative fitness scores as determined by Gene Set Enrichment Analysis. GO Bioprocess terms that meet the significance threshold (padj<0.2) are shown.
SAFE
Lists genes whose neighbors in the global genetic interaction profile similarity network are enriched for single mutant differential fitness defects as determined by SAFE. Significant enrichment (P <0.05) are highlighted in green.

File S3. Raw genetic and differential interaction datasets.

132.7MB

This file contains multiple tabs:

Diagnostic array_complete
The complete genetic and differential interaction data derived from SGA screens in 14 different test conditions using the diagnostic array.
Genome-scale_Benomyl

Lists raw genetic and differential interaction data from genome-wide SGA screens performed in the presence of Benomyl.

These interaction datasets are provided in a tab-delimited format with 25 columns:

  • Query ORF
  • Array ORF
  • Condition
  • Query common name
  • Array common name
  • Genetic interaction score (epsilon)_condition_replicate 1
  • Genetic interaction score (epsilon)_condition_replicate 2
  • Genetic interaction score (epsilon)_condition_mean
  • Genetic interaction_Standard deviation (sd)_condition
  • Genetic interaction_P-value_Condition
  • Genetic interaction score (epsilon)_reference_replicate 1
  • Genetic interaction score (epsilon)_reference_replicate 2
  • Genetic interaction score (epsilon)_reference_mean
  • Genetic interaction_Standard deviation (sd)_reference
  • Genetic interaction_P-value_reference
  • Differential interaction score (epsilon)_condition_replicate 1
  • Differential interaction score (epsilon)_condition_replicate 2
  • Differential interaction score (epsilon)_condition_mean
  • Differential interaction_Standard deviation (sd)
  • Differential interaction_P-value
  • Differential interaction sign
  • Differential Interaction class
  • Query-Array gene pair
  • Genetic interaction score (epsilon) for corresponding gene pair from Costanzo et al 2016 if available
  • Genetic interaction p-value for corresponding gene pair from Costanzo et al 2016 if available
Matched reference screens

Lists genetic interaction data for 4 query mutant strains (TRS20, LSM6, RPN12, and GIM3) screened against the diagnostic array where the resulting double mutant arrays were copied twice and each copy was grown in the standard reference condition, as described above. This configuration was repeated twice to generate two independent biological replicates for each query with two.

This interaction dataset is provided in a tab-delimited format with 9 columns:

  • Query ORF
  • Array ORF
  • Query common name
  • Array common name
  • Biological replicate
  • Matched_replicate1_epsilon
  • Matched_replicate2_epsilon
  • Matched_replicate1_p_value
  • Matched_replicate2_p_value
Degree & Density
Summarizes the number of genetic and differential interactions (i.e. interaction degree) and fraction of genetic and differential interactions identified at the intermediate confidence threshold (P<0.05 and |ε| ≥ 0.08) relative to the total number of gene pairs tested (i.e. interaction density) in each condition.

File S4. MCMC consensus negative and positive genetic interaction profiles.

0.24MB

This file lists consensus, reference condition negative (“consensus negative” tab) and positive (“consensus positive” tab) genetic interactions based on Markov Chain Monte Carlo modeling of biological replicate screens. Gene pairs with an interaction probability greater than 0.5 are shown.

File S5. Functional coherence analysis.

0.28MB

This file lists enrichment for interactions within or between bioprocess clusters represented on the global genetic interaction network. The first tab lists the identity of the 17 biological process network clusters, i.e. “functional neighborhoods”. Multiple tabs are included, each representing a particular enrichment set for different types of interactions.

Query centric GI
Enrichment for negative and positive genetic interactions in the reference condition for each query gene and functional neighborhood pair. The average number of interactions across 14 biological replicates are used.
Query centric Novel
Enrichment for negative and positive novel differential interactions across 14 conditions for each query gene and functional neighborhood pair. The aggregated number of interactions across conditions are used.
Benomyl Novel
Enrichment for negative novel differential interactions on Benomyl for each query gene and functional neighborhood pair. Both screens using either the mini-array or the genome-wide array are included.
Query centric non-signif.

Enrichment for negative differential interactions derived from non-significant genetic interactions both on the reference condition and the test condition for each query gene and functional neighborhood pair. The aggregated number of interactions across conditions are used.

For query centric analyses described above, the enrichment data are provided in a tab-delimited format with 13 columns:

  • Interaction Type
  • Query ORF
  • Query gene name
  • Query functional neighborhood
  • Functional neighborhoods
  • nBackground
  • nRegion
  • nGI
  • nCommon
  • Fold-enrichment
  • P value
  • Odds Ratio
  • Within/Between process
Condition centric Novel
Enrichment for negative novel differential interactions for each condition and functional neighborhood pair. The aggregated number of interactions across 26 query genes are used.
Condition centric non-signif.

Enrichment for negative differential interactions derived from non-significant genetic interactions both on the reference condition and the test condition for each condition and functional neighborhood pair. The aggregated number of interactions across 26 query genes are used.

For condition centric analyses described above, the enrichment data are provided in a tab-delimited format with 12 columns:

  • Interaction Type
  • Condition
  • Functional neighborhood targeted by condition
  • Functional neighborhoods
  • nBackground
  • nRegion
  • nGI
  • nCommon
  • Fold-enrichment
  • P value
  • Odds Ratio
  • Within/Between process