Experiment: Yeast cell cycle (CDC28) MIPS Description # ORFs Average corr. P-value -log(P-value) 01 METABOLISM 1001 0.0285 0.00E+00 NA 01.01 amino-acid metabolism 200 0.0771 0.00E+00 NA 01.01.01 amino-acid biosynthesis 115 0.1506 0.00E+00 NA 01.01.04 regulation of amino-acid metabolism 33 0.0245 3.40E-02 1.5 01.01.07 amino-acid transport 23 0.072 2.00E-04 3.7 01.01.10 amino-acid degradation 35 0.0997 0.00E+00 NA 01.01.99 other amino-acid metabolism activities 4 -0.0667 7.12E-01 0.1 01.02 nitrogen and sulphur metabolism 73 0.0207 1.20E-03 2.9 01.02.01 nitrogen and sulphur utilization 37 0.0312 8.00E-03 2.1 01.02.04 regulation of nitrogen and sulphur utilization 28 0.0019 3.90E-01 0.4 01.02.07 nitrogen and sulphur transport 8 -0.0521 8.62E-01 0.1 01.03 nucleotide metabolism 135 0.0188 0.00E+00 NA 01.03.01 purine-ribonucleotide metabolism 42 0.0539 0.00E+00 NA 01.03.04 pyrimidine-ribonucleotide metabolism 28 0.0825 0.00E+00 NA 01.03.07 deoxyribonucleotide metabolism 12 0.071 3.40E-02 1.5 01.03.10 metabolism of cyclic and unusual nucleotides 8 0.004 4.17E-01 0.4 01.03.13 regulation of nucleotide metabolism 13 -0.001 4.58E-01 0.3 01.03.16 polynucleotide degradation 21 0.0161 1.71E-01 0.8 01.03.19 nucleotide transport 12 -0.0211 7.06E-01 0.2 01.03.99 other nucleotide-metabolism activities 7 0.2465 6.00E-04 3.2 01.04 phosphate metabolism 31 0.0477 2.20E-03 2.7 01.04.01 phosphate utilization 13 0.086 1.00E-02 2.0 01.04.04 regulation of phosphate utilization 8 -0.0168 5.95E-01 0.2 01.04.07 phosphate transport 10 0.0086 3.61E-01 0.4 01.05 carbohydrate metabolism 401 0.0304 0.00E+00 NA 01.05.01 carbohydrate utilization 252 0.0459 0.00E+00 NA 01.05.04 regulation of carbohydrate utilization 118 0.0655 0.00E+00 NA 01.05.07 carbohydrate transport 39 0.0447 6.00E-04 3.2 01.05.99 other carbohydrate metabolism activities 2 0.659 5.60E-03 2.3 01.06 "lipid, fatty-acid and sterol metabolism" 177 0.0288 0.00E+00 NA 01.06.01 "lipid, fatty-acid and sterol biosynthesis" 95 0.0683 0.00E+00 NA 01.06.04 breakdown of lipids and phospholipids 15 -0.0099 6.01E-01 0.2 01.06.07 "lipid, fatty-acid and sterol utilization" 26 0.0188 9.96E-02 1.0 01.06.10 "regulation of lipid, fatty-acid and sterol biosynthesis" 19 -0.0292 9.57E-01 0.0 01.06.13 lipid and fatty-acid transport 17 0.0362 8.02E-02 1.1 01.06.16 lipid and fatty-acid binding 3 0.1507 1.63E-01 0.8 01.06.99 "other lipid, fatty-acid and sterol metabolism proteins" 12 0.0185 2.59E-01 0.6 01.07 "biosynthesis of vitamins, cofactors, and prosthetic groups " 79 0.0416 0.00E+00 NA 01.07.01 "metabolism of vitamins, cofactors, and prosthetic groups " 60 0.0372 0.00E+00 NA 01.07.04 "utilization of vitamins, cofactors, and prosthetic groups " 7 -0.0438 7.55E-01 0.1 01.07.07 "regulation of vitamins, cofactors, and prosthetic groups " 3 0.2012 9.74E-02 1.0 01.07.10 "transport of vitamins, cofactors, and prosthetic groups " 3 0.0385 3.70E-01 0.4 01.07.99 "other vitamin, cofactor, and prosthetic group activities " 6 0.2525 4.00E-04 3.4 01.20 secondary metabolism 4 0.0063 4.42E-01 0.4 01.20.05 amines metabolism 4 0.0063 4.42E-01 0.4 02 ENERGY 220 0.1334 0.00E+00 NA 02.01 glycolysis 26 0.3231 0.00E+00 NA 02.04 gluconeogenesis 9 0.2016 2.00E-04 3.7 02.07 pentose-phosphate pathway 9 0.0908 3.54E-02 1.5 02.10 tricarboxylic-acid pathway 22 0.1333 0.00E+00 NA 02.13 respiration 71 0.2827 0.00E+00 NA 02.16 fermentation 32 0.0216 5.14E-02 1.3 02.19 "metabolism of energy reserves (glycogen, trehalose)" 37 0.0981 0.00E+00 NA 02.22 glyoxylate cycle 6 0.1545 2.44E-02 1.6 02.25 beta-oxidation of fatty acids 5 0.0271 3.45E-01 0.5 02.99 other energy generation activities 13 0.0234 2.01E-01 0.7 03 "CELL GROWTH, CELL DIVISION AND DNA SYNTHESIS" 757 0.0088 0.00E+00 NA 03.01 cell growth 72 0.058 0.00E+00 NA 03.04 "budding, cell polarity and filament formation" 165 0.0689 0.00E+00 NA 03.07 "pheromone response, mating-type determination, sex-specific proteins" 156 0.0097 8.00E-04 3.1 03.10 sporulation and germination 96 -0.0014 5.80E-01 0.2 03.13 meiosis 91 0.0057 8.90E-02 1.1 03.16 DNA synthesis and replication 81 0.0598 0.00E+00 NA 03.19 recombination and DNA repair 86 0.0063 8.30E-02 1.1 03.22 cell cycle control and mitosis 317 0.023 0.00E+00 NA 03.22.01 cell cycle check point proteins 21 0.0512 1.12E-02 2.0 03.25 cytokinesis 30 0.0821 0.00E+00 NA 03.99 "other cell growth, cell division and DNA synthesis activities" 10 -0.0519 9.26E-01 0.0 04 TRANSCRIPTION 708 0.0304 0.00E+00 NA 04.01 rRNA transcription 95 0.1474 0.00E+00 NA 04.01.01 rRNA synthesis 39 0.1103 0.00E+00 NA 04.01.04 rRNA processing 53 0.2027 0.00E+00 NA 04.01.99 other rRNA-transcription activities 3 -0.1287 7.83E-01 0.1 04.03 tRNA transcription 75 0.0453 0.00E+00 NA 04.03.01 tRNA synthesis 24 0.1085 0.00E+00 NA 04.03.03 tRNA processing 36 0.009 1.80E-01 0.7 04.03.06 tRNA modification 11 0.0845 2.06E-02 1.7 04.03.99 other tRNA-transcription activities 4 0.0853 2.05E-01 0.7 04.05 mRNA transcrition 511 0.0285 0.00E+00 NA 04.05.01 mRNA synthesis 394 0.0295 0.00E+00 NA 04.05.01.01 general transcription activities 61 0.0641 0.00E+00 NA 04.05.01.04 transcriptional control 309 0.0336 0.00E+00 NA 04.05.01.07 chromatin modification 30 0.0299 2.12E-02 1.7 04.05.03 mRNA processing (splicing) 73 0.0444 0.00E+00 NA 04.05.05 "mRNA processing (5'-end, 3'-end processing and mRNA degradation)" 36 0.0204 4.20E-02 1.4 04.05.99 other mRNA-transcription activities 10 -0.0347 8.06E-01 0.1 04.07 RNA transport 27 0.0497 3.80E-03 2.4 04.99 other transcription activities 59 0.0115 4.94E-02 1.3 05 PROTEIN SYNTHESIS 328 0.1344 0.00E+00 NA 05.01 ribosomal proteins 189 0.2303 0.00E+00 NA 05.04 "translation (initiation, elongation and termination)" 63 0.1188 0.00E+00 NA 05.07 translational control 28 0.048 3.80E-03 2.4 05.10 tRNA-synthetases 37 0.1317 0.00E+00 NA 05.99 other protein-synthesis activities 12 0.0595 5.46E-02 1.3 06.01 protein folding and stabilization 54 0.0845 0.00E+00 NA 06.04 "protein targeting, sorting and translocation" 119 0.0831 0.00E+00 NA 06.07 "protein modification (glycolsylation, acylation, myristylation, palmitylation, farnesylation and processing) " 164 0.0104 4.00E-04 3.4 06.10 assembly of protein complexes 87 0.1166 0.00E+00 NA 06.13 proteolysis 141 0.086 0.00E+00 NA 06.13.01 cytoplasmic degradation 91 0.0997 0.00E+00 NA 06.13.04 lysosomal and vacuolar degradation 17 0.1164 0.00E+00 NA 06.13.07 other subcellular degradation 14 0.093 4.60E-03 2.3 06.99 other protein-destination activities 5 0.0889 1.47E-01 0.8 07 TRANSPORT FACILITATION 289 0.0511 0.00E+00 NA 07.01 ion channels 7 0.0236 3.16E-01 0.5 07.04 ion transporters 69 0.1254 0.00E+00 NA 07.04.01 "metal ion transporters (Cu, Fe, etc.)" 21 0.0918 0.00E+00 NA 07.04.04 "other cation transporters (Na ,K ,Ca ,NH4 ,etc.)" 34 0.2808 0.00E+00 NA 07.04.07 "anion transporters (Cl, SO4, PO4, etc.)" 16 0.0403 6.00E-02 1.2 07.07 sugar and carbohydrate transporters 42 0.0377 8.00E-04 3.1 07.10 amino-acid transporters 25 0.0928 0.00E+00 NA 07.13 lipid transporters 7 0.1211 3.16E-02 1.5 07.16 purine and pyrimidine transporters 14 -0.0169 7.03E-01 0.2 07.19 allantoin and allantoate transporters 9 0.1331 6.20E-03 2.2 07.22 transport ATPases 38 0.3429 0.00E+00 NA 07.25 ABC transporters 26 0.0538 2.80E-03 2.6 07.28 drug transporters 33 0.0593 8.00E-04 3.1 07.99 other transport facilitators 54 0.0364 0.00E+00 NA 08 INTRACELLULAR TRANSPORT 424 0.0658 0.00E+00 NA 08.01 nuclear transport 48 0.0818 0.00E+00 NA 08.04 mitochondrial transport 71 0.1076 0.00E+00 NA 08.07 "vesicular transport (Golgi network, etc.)" 102 0.0542 0.00E+00 NA 08.10 peroxisomal transport 13 0.1405 2.00E-04 3.7 08.13 vacuolar transport 43 0.189 0.00E+00 NA 08.16 extracellular transport 36 0.0504 8.00E-04 3.1 08.19 cellular import 97 0.069 0.00E+00 NA 08.22 cytoskeleton-dependent transport 27 0.1258 0.00E+00 NA 08.99 other intracellular-transport activities 24 0.1278 0.00E+00 NA 09 CELLULAR BIOGENESIS (proteins are not localized to the corresponding organelle) 163 0.0069 9.80E-03 2.0 09.01 biogenesis of cell wall 97 -0.0016 6.04E-01 0.2 09.04 biogenesis of cytoskeleton 17 0.0585 1.90E-02 1.7 09.07 biogenesis of endoplasmatic reticulum 3 -0.0458 5.86E-01 0.2 09.08 biogenesis of Golgi 2 -0.2042 7.82E-01 0.1 09.10 nuclear biogenesis 5 0.2835 3.00E-03 2.5 09.13 biogenesis of chromosome structure 17 -0.0206 8.05E-01 0.1 09.16 mitochondrial biogenesis 10 0.072 5.30E-02 1.3 09.19 peroxisomal biogenesis 2 0.3418 1.06E-01 1.0 09.25 vacuolar and lysosomal biogenesis 13 0.0144 2.77E-01 0.6 10 SIGNAL TRANSDUCTION 122 0.0107 3.20E-03 2.5 10.02 morphogenesis 27 0.0284 4.26E-02 1.4 10.02.07 G-proteins 3 0.2625 4.84E-02 1.3 10.02.09 regulation of G-protein activity 5 -0.1483 9.83E-01 0.0 10.02.11 key kinases 8 0.0054 4.06E-01 0.4 10.02.99 other morphogenetic activities 11 -0.0012 4.65E-01 0.3 10.03 osmosensing 17 0.0307 1.05E-01 1.0 10.03.05 mediator proteins 3 0.2467 5.68E-02 1.2 10.03.11 key kinases 8 0.1245 2.04E-02 1.7 10.03.13 key phosphatases 2 -0.2888 8.62E-01 0.1 10.03.99 other osmosensing activities 4 -0.1966 9.84E-01 0.0 10.04 nutritional response pathway 22 0.0217 1.13E-01 0.9 10.04.07 G-proteins 3 -0.2729 9.75E-01 0.0 10.04.09 regulation of G-protein activity 4 0.0332 3.48E-01 0.5 10.04.11 key kinases 2 -0.2459 8.26E-01 0.1 10.04.13 key phosphatases 2 0.1094 3.46E-01 0.5 10.04.99 other nutritional-response activities 9 -0.0466 8.70E-01 0.1 10.05 pheromone response generation 34 -0.0085 7.56E-01 0.1 10.05.01 receptor proteins 2 -0.4222 9.40E-01 0.0 10.05.07 G-proteins 7 0.0658 1.35E-01 0.9 10.05.09 regulation of G-protein activity 2 0.5494 1.88E-02 1.7 10.05.11 key kinases 4 -0.1345 9.07E-01 0.0 10.05.99 other pheromone response activities 18 -0.0068 5.72E-01 0.2 10.99 other signal-transduction activities 37 0.013 1.10E-01 1.0 11 "CELL RESCUE, DEFENSE, CELL DEATH AND AGEING " 331 0.008 0.00E+00 NA 11.01 stress response 149 0.0284 0.00E+00 NA 11.04 "DNA repair (direct repair, base excision repair and nucleotide excision repair)" 80 0.0207 2.00E-04 3.7 11.07 detoxificaton 93 0.0263 0.00E+00 NA 11.07.01 detoxification involving cytochrome P450 4 -0.2631 9.99E-01 0.0 11.10 cell death 10 -0.0255 7.17E-01 0.1 11.11 ageing 2 0.6911 4.40E-03 2.4 11.99 other cell rescue activities 9 0.031 2.34E-01 0.6 13 IONIC HOMEOSTASIS 114 0.0932 0.00E+00 NA 13.01 homeostasis of metal ions 55 0.0849 0.00E+00 NA 13.04 homeostasis of other ions 60 0.1539 0.00E+00 NA 30 CELLULAR ORGANIZATION (proteins are localized to the corresponding organelle) 2088 0.0403 0.00E+00 NA 30.01 organization of cell wall 29 -0.0056 6.15E-01 0.2 30.02 organization of plasma membrane 137 0.0249 0.00E+00 NA 30.03 organization of cytoplasm 549 0.1147 0.00E+00 NA 30.04 organization of cytoskeleton 94 0.0621 0.00E+00 NA 30.05 organization of centrosome 28 0.1509 0.00E+00 NA 30.07 organization of endoplasmatic reticulum 115 0.0752 0.00E+00 NA 30.08 organization of Golgi 66 0.0916 0.00E+00 NA 30.09 organization of intracellular transport vesicles 42 0.1215 0.00E+00 NA 30.10 nuclear organization 720 0.0241 0.00E+00 NA 30.13 organization of chromosome structure 41 0.1104 0.00E+00 NA 30.16 mitochondrial organization 320 0.2034 0.00E+00 NA 30.19 peroxisomal organization 37 0.108 0.00E+00 NA 30.22 endosomal organization 8 0.08 7.54E-02 1.1 30.25 vacuolar and lysosomal organization 47 0.1575 0.00E+00 NA 30.90 extracellular/secretion proteins 20 0.0682 3.80E-03 2.4 30.99 other cellular organization 4 0.1709 7.14E-02 1.1 90 RETROTRANSPOSONS AND PLASMID PROTEINS 6 -0.1304 9.91E-01 0.0 98 CLASSIFICATION NOT YET CLEAR-CUT 146 0.0092 4.60E-03 2.3