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Table 1 Enriched variations

From: Mining for genotype-phenotype relations in Saccharomyces using partial least squares

Label Phenotype N Ess. genes Paralog Frame shifts Stop codon Copy no.
Mel_R Melibiose 2% Rate 33 0 2.06* 0.25 1.23 4.41*
Mel_E Melibiose 2% Efficiency 40 0 0.78 0.20 1.37 3.59
Cup_R Cupper chloride 0.375 mM Rate 60 0.16 2.56***••• 0.15 1.63 6.42***•••
Cup_E Cupper chloride 0.375 mM Efficiency 14 0 2.19 0.11 3.36* 11.42**•
NaC1_R NaCl 0.85 M Rate 58 0.16 2.91***••• 0.05 1.16 8.25***•••
NaC2_R NaCl 1.25 M Rate 47 0.31 1.12 0.13 1.46 0
NaC1_E NaCl 0.85 M Efficiency 47 0.01 2.34***•• 0.13 1.46 12.70***•••
NaC2_E NaCl 1.25 M Efficiency 43 0.11 1.25 0.14 0.92 3.33
Mal_R Maltose 2% Rate 59 0.51 2.05**•• 0.19 1.39 11.50***•••
Mal_E Maltose 2% Efficiency 45 0.32 1.37 0.21 0.87 13.37***•••
Gal_R Galactose 2% Rate 30 0 1.67 0 0.88 22.11***•••
Gal_E Galactose 2% Efficiency 49 0.19 2.67***••• 0.27 1.40 22.11***•••
Hea1_R Heat 37°C Rate 33 0 2.06*• 0.09 2.20* 9.65***•••
Hea2_R Heat 40°C Rate 44 0 2.06**• 0.07 1.23 13.73***•••
Hea1_E Heat 37°C Efficiency 44 0.11 1.21 0.26 1.58 1.568
Hea2_E Heat 40°C Efficiency 49 0.40 1.78* 0.12 1.72 9.99***•••
Sod1_R Sodium arsenite oxide 3.5 mM Rate 48 0 5.58***••• 0.13 2.11*• 12.38***•••
Sod2_R Sodium arsenite oxide 5 mM Rate 33 0.29 3.15***•• 0.09 2.20* 2.11
Sod1_E Sodium arsenite oxide 3.5 mM Efficiency 44 0.22 1.83* 0.18 1.95 13.73***•••
Sod2_E Sodium arsenite oxide 5 mM Efficiency 43 0 3.62***••• 0.14 2.40**• 3.33
  1. Certain types of variations that are over-represented among the N influential genes for all phenotypes. The statistics are odds-ratios indicating potential enrichment of certain gene categories among the influential genes. The categories are: Essential genes, genes with known paralogs, genes with known frame shift variation, genes with known stop codon variation and genes with known copy number variations in yeast. Significance at 10% is marked with *, 5% is marked with ** and 1% is marked with ***. The corresponding significance based on adjusted p-values controlling the false discovery rate (q-values) are marked with , •• and •••, respectively.