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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]
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Microbial Cell Factories

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