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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.