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Table 3 Distribution of selected genes versus all S. cerevisiae genes

From: Large-scale exploration of growth inhibition caused by overexpression of genomic fragments in Saccharomyces cerevisiae

 

All S. cerevisiae genes

Percentage of total

Selected toxic genes

Percentage of total

Functional classes (MIPS data)

    

Cell cycle_DNA processing

670

11.5

75

16.5*

Cell fate

486

8.4

66

14.5*

Cell rescue, defense and virulence

288

5.0

23

5.1

Cellular communication/signal transduction mechanism

59

1.0

6

1.3

Cellular transport and transport mechanisms

525

9.0

67

14.8*

Classification not yet clear-cut

112

1.9

6

1.3

Control of cellular organization

207

3.6

22

4.8

Energy

244

4.2

12

2.6

Metabolism

1,061

18.3

88

19.4

Protein fate (folding, modification, destination)

593

10.2

47

10.4

Protein synthesis

377

6.5

17

3.7*

Regulation of/interaction with cell. Environment

197

3.4

29

6.4

Transcription

801

13.8

88

19.4*

Transport facilitation

321

5.5

61

13.4*

Unclassified

1,706

29.4

91

20.0*

Cellular localization (MIPS data)

    

Extracellular

54

1.4

5

1.6

Cell wall

38

1.0

4

1.3

Golgi

103

2.6

8

2.5

Transport vesicles

54

1.4

3

0.9

Plasma membrane

171

4.4

34

10.7*

Nucleus

1,367

34.8

130

40.8

Cytoplasm

2,001

50.9

137

42.9*

Peroxisome

42

1.1

3

0.9

Endosome

20

0.5

2

0.6

Cytoskeleton

154

3.9

22

6.9

Vacuole

82

2.1

8

2.5

Endoplasmic reticulum

353

9.0

27

8.5

Mitochondria

562

14.3

37

11.6

Viability (MIPS data)

    

Essential

939

16.2

96

21.1

Essential or not

160

2.8

20

4.4

Phylogeny (Génolevures data)

    

Conserved

3,717

64.1

336

74.0*

Ascomycete-specifics

1674

28.8

106

23.3*

Orphan

412

7.1

10

2.2*

  1. The distribution of genes was examined in respect of four classifications: function, cellular localization of the gene product, viability and phylogeny. Data are from MIPS [38] and Génolevures [37]. Cellular localization was known for 3,928 out of the 5,803 proteins in the entire genome and for 319 proteins out of the 454 that yield toxic inserts. For other comparisons, the set of 454 selected genes was compared to the set of 5,803 genes of S. cerevisiae. Note that a given gene may be present in more than one MIPS class. Significant evidence that a given gene class is over-or under-represented among toxic genes as compared to all S. cerevisiae genes is emphasized by bold characters. *p < 0.005; p < 0.025.