TABLE 1.

Enrichment of transcription factor motifs (TFMs) and MIPS functional categories in clusters of genes that were differentially expressed in response to anaerobiosis in galactose medium (wild-type strain, SOM clustering with 1D ring topology)

Cluster no.naTFMReference(s)Percentage sharePMIPS functional categoryPd (genomic)
In setbGenomicc
155MCB58, 91658.97.9Cell cycle and DNA processing7.6
SCB91474.94.5DNA synthesis and replication7.0
MBP146, 54, 764510.4≥38Nucleus4.8
SWI446, 54, 76452.73.3DNA recombination and DNA repair2.7
SWI646, 54458.411.1
270RRPE46374.98.8Translation2.3
rRNA transcription2.1
378PAC467411.719.1rRNA processing/transcription≥5.0
RRPE46417.2≥38tRNA synthesis2.5
ABF146, 54, 76, 91462.12.7Polynucleotide degradation2.4
456PAC467910.316.1Pyrimidine ribonucleotide metabolism2.7
RRPE465410.315.3rRNA transcription2.6
ABF191522.73.3
551PAC46572.75.8Nucleotide metabolism2.2
RRPE46312.34.5
618
743HAP146, 76, 85, 91303.65.0Mitochondrion/respiration/energy≥4.6
INO246302.82.7
848MAC146402.83.6Mitochondrion/respiration/energy≥5.7
HAP2/3/4/546332.33.4Mitochondrial transport5.4
Homeostasis of cations4.0
Cellular transport and transport mechanisms2.4
976Ribosome biogenesis11.3
Protein synthesis10.0
Mitochondrion/respiration/energy≥3.7
1030
1174MSN2/491682.94.4C-compound, carbohydrate transport/metabolism≥4.7
MIG146283.64.0Metabolism of energy reserves (glycogen, trehalose)3.1
1291MSN2/491642.43.9C-compound, carbohydrate transport/metabolism≥5.9
Proteolytic degradation5.6
Metabolism of energy reserves (glycogen, trehalose)4.9
C-compound & carbohydrate utilization2.4
1347INO276872.1NSeC-compound & carbohydrate metabolism3.1
MIG146192.12.7Metabolism of energy reserves (glycogen, trehalose)2.7
Cell rescue, defense and virulence2.6
1432GCR176502.12.3Nitrogen & sulfur metabolism6.1
PHO446, 76, 91502.43.0Amino acid metabolism4.2
ACE254, 91442.52.9Lipid, fatty acid & isoprenoid metabolism activities2.7
C-compound & carbohydrate utilization2.0
1529MAC146452.63.2Lipid, fatty acid & isoprenoid metabolism2.6
UPC216212.33.8Tricarboxylic acid pathway2.2
Phosphate metabolism2.0
1671ROX117893.93.5Cell rescue, defense & virulence8.1
UPC2167018.821.4Cell wall5.5
ABC transporters2.4
1715HAP2/3/4/554332.22.7Lipid, fatty acid & isoprenoid metabolism8.1
UPC216272.13.1Endoplasmic reticulum4.6
054HAP2/3/4/546112.43.7rRNA transcription2.6
Mitochondrion/respiration/energy≥2.3
Vitamin, cofactor & prosthetic group biosynthesis/metabolism≥2.2
  • a n = number of genes in cluster.

  • b Hypergeometric P [−log10(p)] for TFM enrichment relative to clustered genes (938).

  • c Hypergeometric P [−log10(p)] for TFM enrichment relative to genome.

  • d Hypergeometric P [−log10(p)] for MIPS functional category enrichment.NS, not significant.

  • e NS, not significant.