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Table 3 Biological process upregulated in vitro

From: The molecular portrait of in vitro growth by meta-analysis of gene-expression profiles

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