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Table 1 Overrepresentation of functional categories among the two clusters of differentially expressed genes (see Fig. 5)

From: Maintenance-energy requirements and robustness of Saccharomyces cerevisiae at aerobic near-zero specific growth rates

  

Functional category

Ka

Nb

p valuec

Cluster 1

MIPSd

Protein synthesis

138

511

4.98·10−31

Ribosomal proteins

95

277

4.29·10−29

Ribosome biogenesis

106

343

2.46·10−28

Amino acid metabolism

69

243

3.31·10−15

Metabolism

221

1530

5.87·10−11

Metabolism of the aspartate family

26

64

1.75·10−8

Metabolism of methionine

18

36

3.52·10−7

Tetracyclic and pentacyclic triterpenes metabolism

16

36

2.84·10−5

Purine nucleotide/nucleoside/nucleobase metabolism

22

66

4.58·10−5

Nucleotide/nucleoside/nucleobase metabolism

48

230

4.81·10−5

Isoprenoid metabolism

16

41

2.55·10−4

Sulfur metabolism

7

8

3.51·10−4

Sulfate assimilation

7

8

3.51·10−4

Metabolism of the cysteine-aromatic group

23

80

4.79·10−4

Aminoacyl-tRNA-synthetases

15

39

7.46·10−4

Energy

58

360

1.69·10−2

Pentose-phosphate pathway

10

24

2.20·10−2

GOd

Translation

117

345

6.31·10−36

Cellular amino acid biosynthetic process

44

101

1.10·10−16

Ribosome biogenesis

46

178

1.13·10−7

Oxidation reduction

60

270

1.24·10−7

Metabolic process

76

389

2.49·10−7

Steroid biosynthetic process

15

24

2.73·10−7

Sterol biosynthetic process

15

28

5.46·10−6

Methionine biosynthetic process

16

32

6.13·10−6

Maturation of SSU-rRNA

22

62

2.28·10−5

Sulfate assimilation

9

11

3.49·10−5

rRNA processing

43

195

8.44·10−5

Methionine metabolic process

10

15

1.36·10−4

Lipid biosynthetic process

18

52

7.16·10−4

Ergosterol biosynthetic process

7

9

2.66·10−3

TFd

FHL1

75

208

1.64·10−24

RAP1

51

145

1.31·10−15

SFP1

20

50

1.41·10−6

GCN4

37

182

8.70·10−4

HAP1

27

120

2.60·10−3

MET32

9

24

4.06·10−2

Cluster 2

MIPSd

Unclassified proteins

194

1140

4.13·10−5

Oxidative stress response

21

56

7.17·10−4

Cell rescue, defense and virulence

101

558

9.06·10−3

Degradation of polyamines

5

5

1.98·10−2

Energy

70

360

2.14·10−2

Cellular communication

50

239

4.60·10−2

Cellular signalling

44

202

4.71·10−2

GOd

Signal transduction

24

74

4.64·10−3

Protein amino acid phosphorylation

36

141

1.11·10−2

Proteasomal ubiquitin-dependent protein catabolic process

9

16

3.95·10−2

Oxidation reduction

56

270

3.96·10−2

Negative regulation of gluconeogenesis

7

10

4.55·10−2

TFd

MSN2/MSN4 e

55

166

4.29·10−11

SKN7

43

175

6.59·10−4

YAP7

36

152

9.78·10−3

CAD1

12

32

4.40·10−2

  1. aNumber of genes present in both the cluster and the functional category
  2. bTotal number of genes in the functional category
  3. cA Bonferroni corrected p value cut-off of 0.05 was used and p values indicate the probability of finding the same number of genes in a random set
  4. dFunctional categories originate from the Munich Information Centre for Protein Sequences (MIPS), Gene Ontology (GO) or transcription factor binding datasets (TF) described in the “Methods” section
  5. eMSN2/4 transcription factor dataset originates from [30]