Table 3.
Biological process upregulated in vitro
| GO category | Total number of genes | Genes changed | Log10 (p-value) | FDR | GO ID |
| Translation | |||||
| Translation | 76 | 36 | -7.95 | 0.0000 | GO:0043037 |
| Ribosome biogenesis and assembly | 42 | 19 | -4.10 | 0.0037 | GO:0042254 |
| Ribosome biogenesis | 41 | 19 | -4.27 | 0.0000 | GO:0007046 |
| Regulation of translation | 33 | 14 | -2.81 | 0.0077 | GO:0006445 |
| Translational initiation | 23 | 13 | -4.20 | 0.0042 | GO:0006413 |
| tRNA metabolism | 27 | 12 | -2.69 | 0.0070 | GO:0006399 |
| tRNA modification | 23 | 11 | -2.82 | 0.0078 | GO:0006400 |
| tRNA aminoacylation for protein translation | 21 | 10 | -2.59 | 0.0125 | GO:0006418 |
| tRNA aminoacylation | 21 | 10 | -2.59 | 0.0125 | GO:0043039 |
| rRNA processing | 17 | 10 | -3.53 | 0.0056 | GO:0006364 |
| rRNA metabolism | 17 | 10 | -3.53 | 0.0056 | GO:0016072 |
| Regulation of translational initiation | 14 | 8 | -2.79 | 0.0075 | GO:0006446 |
| Translational elongation | 14 | 7 | -2.07 | 0.0400 | GO:0006414 |
| Transcription from Pol I promoter | 7 | 5 | -2.44 | 0.0141 | GO:0006360 |
| Splicing | |||||
| RNA processing | 123 | 52 | -9.02 | 0.0000 | GO:0006396 |
| RNA metabolism | 130 | 52 | -8.00 | 0.0000 | GO:0016070 |
| mRNA metabolism | 64 | 21 | -2.27 | 0.0217 | GO:0016071 |
| mRNA processing | 57 | 20 | -2.56 | 0.0123 | GO:0006397 |
| RNA splicing | 41 | 18 | -3.70 | 0.0030 | GO:0008380 |
| RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 33 | 15 | -3.37 | 0.0050 | GO:0000377 |
| RNA splicing, via transesterification reactions | 33 | 15 | -3.37 | 0.0050 | GO:0000375 |
| Nuclear mRNA splicing, via spliceosome | 33 | 15 | -3.37 | 0.0050 | GO:0000398 |
| RNA modification | 25 | 11 | -2.46 | 0.0143 | GO:0009451 |
| Nucleotide metabolism | |||||
| Nucleobase, nucleoside, nucleotide and nucleic acid metabolism | 806 | 192 | -4.43 | 0.0000 | GO:0006139 |
| Nucleotide metabolism | 61 | 20 | -2.18 | 0.0304 | GO:0009117 |
| Nucleotide biosynthesis | 45 | 16 | -2.21 | 0.0303 | GO:0009165 |
| Ribonucleotide metabolism | 28 | 13 | -3.09 | 0.0047 | GO:0009259 |
| Ribonucleotide biosynthesis | 27 | 13 | -3.28 | 0.0048 | GO:0009260 |
| Purine nucleotide metabolism | 29 | 12 | -2.37 | 0.0164 | GO:0006163 |
| Purine nucleotide biosynthesis | 26 | 12 | -2.86 | 0.0080 | GO:0006164 |
| Purine ribonucleotide metabolism | 25 | 11 | -2.46 | 0.0143 | GO:0009150 |
| Purine ribonucleotide biosynthesis | 24 | 11 | -2.63 | 0.0115 | GO:0009152 |
| Nucleoside triphosphate metabolism | 23 | 10 | -2.23 | 0.0299 | GO:0009141 |
| Ribonucleoside triphosphate metabolism | 20 | 9 | -2.17 | 0.0295 | GO:0009199 |
| Ribonucleoside triphosphate biosynthesis | 19 | 9 | -2.35 | 0.0167 | GO:0009201 |
| Nucleoside triphosphate biosynthesis | 20 | 9 | -2.17 | 0.0295 | GO:0009142 |
| Purine ribonucleoside triphosphate metabolism | 20 | 9 | -2.17 | 0.0295 | GO:0009205 |
| Purine ribonucleoside triphosphate biosynthesis | 19 | 9 | -2.35 | 0.0167 | GO:0009206 |
| Purine nucleoside triphosphate metabolism | 21 | 9 | -2.00 | 0.0413 | GO:0009144 |
| Purine nucleoside triphosphate biosynthesis | 19 | 9 | -2.35 | 0.0167 | GO:0009145 |
| Nucleoside metabolism | 14 | 7 | -2.07 | 0.0400 | GO:0009116 |
| Protein modifiication and degradation | |||||
| Protein metabolism | 836 | 210 | -6.86 | 0.0000 | GO:0019538 |
| Protein biosynthesis | 207 | 72 | -7.76 | 0.0000 | GO:0006412 |
| Intracellular transport | 176 | 63 | -7.36 | 0.0000 | GO:0046907 |
| Protein transport | 149 | 52 | -5.75 | 0.0000 | GO:0015031 |
| Intracellular protein transport | 138 | 50 | -6.11 | 0.0000 | GO:0006886 |
| Amino acid and derivative metabolism | 126 | 36 | -2.31 | 0.0198 | GO:0006519 |
| Amino acid metabolism | 98 | 29 | -2.19 | 0.0297 | GO:0006520 |
| Ubiquitin-dependent protein catabolism | 48 | 26 | -7.39 | 0.0000 | GO:0006511 |
| Modification-dependent protein catabolism | 48 | 26 | -7.39 | 0.0000 | GO:0019941 |
| Protein targeting | 70 | 23 | -2.44 | 0.0139 | GO:0006605 |
| Protein folding | 46 | 22 | -5.14 | 0.0000 | GO:0006457 |
| Ubiquitin cycle | 31 | 12 | -2.10 | 0.0351 | GO:0006512 |
| Amino acid activation | 21 | 10 | -2.59 | 0.0125 | GO:0043038 |
| Polyamine metabolism | 5 | 4 | -2.27 | 0.0271 | GO:0006595 |
| Metabolism | |||||
| Metabolism | 2008 | 457 | -12.88 | 0.0000 | GO:0008152 |
| Biosynthesis | 423 | 119 | -6.33 | 0.0000 | GO:0009058 |
| Energy pathways | 128 | 38 | -2.74 | 0.0074 | GO:0006091 |
| Energy derivation by oxidation of organic compounds | 89 | 32 | -4.02 | 0.0036 | GO:0015980 |
| Main pathways of carbohydrate metabolism | 56 | 20 | -2.67 | 0.0069 | GO:0006092 |
| Coenzyme and prosthetic group metabolism | 55 | 18 | -2.00 | 0.0419 | GO:0006731 |
| Coenzyme metabolism | 44 | 16 | -2.32 | 0.0200 | GO:0006732 |
| Glucose catabolism | 30 | 12 | -2.23 | 0.0307 | GO:0006007 |
| Coenzyme and prosthetic group biosynthesis | 31 | 12 | -2.10 | 0.0351 | GO:0046138 |
| Oxidative phosphorylation | 13 | 11 | -6.25 | 0.0000 | GO:0006119 |
| Coenzyme biosynthesis | 23 | 10 | -2.23 | 0.0299 | GO:0009108 |
| Cellular respiration | 11 | 9 | -4.94 | 0.0000 | GO:0045333 |
| Aerobic respiration | 9 | 8 | -4.92 | 0.0000 | GO:0009060 |
| Tricarboxylic acid cycle | 18 | 8 | -1.94 | 0.0462 | GO:0006099 |
| ATP synthesis coupled electron transport (sensu Eukarya) | 6 | 5 | -2.91 | 0.0061 | GO:0042775 |
| ATP synthesis coupled electron transport | 6 | 5 | -2.91 | 0.0061 | GO:0042773 |
| Cell-cycle progression | |||||
| Cell cycle | 324 | 89 | -4.32 | 0.0000 | GO:0007049 |
| Cell organization and biogenesis | 315 | 83 | -3.38 | 0.0054 | GO:0016043 |
| DNA metabolism | 188 | 64 | -6.53 | 0.0000 | GO:0006259 |
| Mitotic cell cycle | 153 | 58 | -7.84 | 0.0000 | GO:0000278 |
| Cytoplasm organization and biogenesis | 202 | 55 | -2.73 | 0.0073 | GO:0007028 |
| DNA replication and chromosome cycle | 83 | 30 | -3.85 | 0.0033 | GO:0000067 |
| M phase | 62 | 26 | -4.68 | 0.0000 | GO:0000279 |
| Nuclear organization and biogenesis | 79 | 25 | -2.36 | 0.0176 | GO:0006997 |
| DNA packaging | 69 | 25 | -3.31 | 0.0049 | GO:0006323 |
| S phase of mitotic cell cycle | 72 | 25 | -3.00 | 0.0043 | GO:0000084 |
| Chromosome organization and biogenesis (sensu Eukarya) | 77 | 24 | -2.20 | 0.0300 | GO:0007001 |
| DNA replication | 67 | 23 | -2.72 | 0.0071 | GO:0006260 |
| Nuclear division | 54 | 22 | -3.82 | 0.0031 | GO:0000280 |
| Establishment and/or maintenance of chromatin architecture | 64 | 21 | -2.27 | 0.0217 | GO:0006325 |
| M phase of mitotic cell cycle | 45 | 20 | -4.15 | 0.0040 | GO:0000087 |
| DNA repair | 59 | 20 | -2.36 | 0.0173 | GO:0006281 |
| Mitosis | 42 | 19 | -4.10 | 0.0037 | GO:0007067 |
| Microtubule-based process | 45 | 19 | -3.61 | 0.0059 | GO:0007017 |
| DNA-dependent DNA replication | 35 | 15 | -3.04 | 0.0044 | GO:0006261 |
| Microtubule cytoskeleton organization and biogenesis | 27 | 14 | -3.94 | 0.0034 | GO:0000226 |
| G1/S transition of mitotic cell cycle | 35 | 13 | -2.06 | 0.0396 | GO:0000082 |
| G2/M transition of mitotic cell cycle | 21 | 9 | -2.00 | 0.0413 | GO:0000086 |
| M-phase specific microtubule process | 12 | 7 | -2.56 | 0.0132 | GO:0000072 |
| Chromosome segregation | 14 | 7 | -2.07 | 0.0400 | GO:0007059 |
| Microtubule nucleation | 9 | 6 | -2.65 | 0.0117 | GO:0007020 |
| DNA replication initiation | 10 | 6 | -2.32 | 0.0190 | GO:0006270 |
| Spindle assembly | 8 | 6 | -3.05 | 0.0045 | GO:0007051 |
| Tubulin folding | 9 | 6 | -2.65 | 0.0117 | GO:0007021 |
| Mitotic spindle assembly | 6 | 5 | -2.91 | 0.0061 | GO:0007052 |
| Pre-replicative complex formation and maintenance | 5 | 4 | -2.27 | 0.0271 | GO:0006267 |
| Chromatin modifications | |||||
| Histone modification | 12 | 7 | -2.56 | 0.0132 | GO:0016570 |
| Covalent chromatin modification | 12 | 7 | -2.56 | 0.0132 | GO:0016569 |
| Others | |||||
| Physiological process | 2917 | 574 | -3.84 | 0.0032 | GO:0007582 |
| Macromolecule biosynthesis | 345 | 100 | -5.98 | 0.0000 | GO:0009059 |
| Response to endogenous stimulus | 77 | 23 | -1.89 | 0.0486 | GO:0009719 |
| Response to DNA damage stimulus | 71 | 22 | -2.02 | 0.0412 | GO:0006974 |