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 |