Skip to main content

Table 4 Main specific gene ontology categories observed in clusters derived from union PPPI network

From: Transcriptional profiling of Saccharomyces cerevisiae exposed to propolis

  Biological process GOID P-valuea Corrected P valueb kc ƒd
Cluster 1 Translation 6416 2.07 x 10-45 2.93 x 10-43 45 499
  Ribosome assembly 42255 1.82 x 10-9 2.58 x 10-8 9 65
  Negative regulation of mRNA processing 50686 8.25 x 10-3 3.90 x 10-2 1 1
Cluster 2 Organic acid transport 15849 2.0594 x 10-4 1.4107 x 10-2 3 65
  Choline transport 15871 1.8904 x 10-3 3.2372 x 10-2 1 1
  Betaine transport 15838 1.8904 x 10-3 3.2372 x 10-2 1 1
  Ethanolamine transport 34229 1.8904 x 10-3 3.2372 x 10-2 1 1
  Amino acid transport 6865 3.4951 x 10-3 4.7047 x 10-2 2 48
Cluster 3 Mitochondrial transport 6839 1.74 x 10-10 3.88 x 10-9 5 67
  Mitochondrion organization and biogenesis 7005 2.6080 x 10-8 2.9122 x 10-7 5 179
  Protein transport 15031 3.7859 x 10-6 2.1138 x 10-5 5 481
  Membrane organization and biogenesis 16044 3.5801 x 10-4 1.0903 x 10-3 3 196
Cluster 4 Transcription from RNA polymerase II promoter 6366 3.4996 x 10-11 3.4296 x 10-9 9 162
  Histone modification 16570 1.1400 x 10-9 2.2345 x 10-8 7 92
  Establishment and/or maintenance of chromatin architecture 6325 2.4536 x 10-9 4.3719 x 10-8 9 260
  Transcription, DNA-dependent 6351 5.8940 x 10-9 8.7746 x 10-8 9 287
  G1 phase of mitotic cell cycle 80 1.0490 x 10-8 1.2850 x 10-7 5 32
  Regulation of RNA metabolic process 51252 1.5270 x 10-8 1.5753 x 10-7 11 614
  Chromosome organization and biogenesis 7001 1.0393 x 10-7 8.8567 x 10-7 9 398
  Response to drug 17035 3.3259 x 10-3 1.1436 x 10-2 3 121
  Cell cycle 7049 1.1244 x 10-2 3.5546 x 10-2 5 566
Cluster 5 DNA catabolic process 6308 7.6846 x 10-5 6.1477 x 10-4 2 30
  Meiotic recombination 7145 2.8107 x 10-4 1.6864 x 10-3 2 57
  Double-strand break repair 6302 3.0125 x 10-4 1.7012 x 10-3 2 59
  M phase of meiotic cell cycle 51327 2.6749 x 10-3 7.7814 x 10-3 2 176
  Telomere maintenance via recombination 722 9.7652 x 10-3 2.5337 x 10-2 1 19
Cluster 6 ER to Golgi vesicle-mediated transport 6888 6.1201 x 10-4 2.5773 x 10-2 2 84
Cluster 7 Negative regulation of RNA metabolic process 51253 2.4984 x 10-6 8.0002 x 10-5 4 157
  Negative regulation of transcription 16481 3.1251 x 10-6 8.0002 x 10-5 4 166
  Heterochromatin formation 31507 3.7388 x 10-5 2.9910 x 10-4 3 92
  Chromatin silencing 6342 3.7388 x 10-5 2.9910 x 10-4 3 92
  Gene silencing 16458 5.4046 x 10-5 3.8433 x 10-4 3 104
  Chromatin modification 16568 5.8205 x 10-4 2.8655 x 10-3 3 231
  Regulation of cell cycle 74 7.1144 x 10-3 1.5701 x 10-2 2 160
Cluster 8 RNA biosynthetic process 32774 2.4585 x 10-3 1.8302 x 10-2 2 289
  Transcription 6350 1.0545 x 10-2 4.8996 x 10-2 2 598
Cluster 9 Intracellular pH reduction 51452 4.8791 x 10-5 6.6815 x 10-4 2 24
  Vacuolar acidification 7035 4.8791 x 10-5 6.6815 x 10-4 2 24
  Regulation of intracellular pH 51453 5.3028 x 10-5 6.6815 x 10-4 2 25
  Proton transport 15992 1.1756 x 10-4 9.1538 x 10-4 2 37
  Cellular homeostasis 19725 2.1588 x 10-3 6.8004 x 10-3 2 158
  Ion transport 6811 2.3248 x 10-3 6.9745 x 10-3 2 164
  ATP metabolic process 46034 1.2324 x 10-2 2.9858 x 10-2 1 24
Cluster 10 Histone methylation 16571 1.2655 x 10-9 1.0504 x 10-7 5 17
  Regulation of transcription 45449 5.8795 x 10-8 2.0914 x 10-6 12 631
  Post-translational protein modification 43687 3.6875 x 10-7 3.9921 x 10-6 10 454
  Chromosome organization and biogenesis 7001 1.7266 x 10-5 9.3463 x 10-5 8 398
  Regulation of conjugation with cellular fusion 31137 4.4395 x 10-3 1.3481 x 10-2 2 31
  Ethanol biosynthetic process during fermentation 43458 6.5202 x 10-3 1.7647 x 10-2 1 2
  Response to stress 6950 1.2590 x 10-2 2.9574 x 10-2 6 632
  Glycolytic fermentation 19660 2.2645 x 10-2 4.6218 x 10-2 1 7
Cluster 11 Chromosome organization and biogenesis 7001 1.1865 x 10-3 2.9377 x 10-2 5 398
  DNA repair 6281 1.2413 x 10-3 2.9377 x 10-2 4 228
  Mitotic cell cycle 278 3.2147 x 10-3 4.5671 x 10-2 4 295
  Histone acetylation 16573 3.4260 x 10-3 4.5671 x 10-2 2 40
  1. a P values were calculated by the hypergeometric distribution of one ontology class visualized in the network.
  2. b Calculated values based on P values obtained after FDR was applied.
  3. c Total number of proteins found in the network which belong to a gene ontology.
  4. d Total number of proteins that belong to a specific gene ontology.