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Table 1 Overrepresentation of MIPS functional categories in genes that were differentially transcribed in response to fully fermentative conditions. Clusters A&B, 2 & 3 and 4, 5 & 6 had similar expression pattern and similar enrichments, and were therefore pooled before the overrepresentation analysis. Enrichment was estimated by hypergeometric distribution analysis (cut-offs around 10-5, see Materials and Methods); magnitude of the enrichment is indicated by the p-value.

From: New insights into the Saccharomyces cerevisiae fermentation switch: Dynamic transcriptional response to anaerobicity and glucose-excess

MIPS_cat.    A&B (283 genes) C (237 genes) D (87 genes)
nr. description nr of genesa nr of genesb p-value nr of genesb p-value nr of genesb p-value
01 METABOLISM 1531      38 3.8E-05
01.01    amino acid metabolism 243 28 2.6E-06 29 1.7E-08   
01.01.06 metabolism of the aspartate family 64    13 4.5E-07   
01.01.06.05.01 biosynthesis of methionine 14    5 1.0E-04   
01.03    nucleotide metabolism 230 23 6.3E-05 23 1.2E-05   
01.03.01 purine nucleotide metabolism 66    17 3.8E-09   
01.03.01.03 purine nucleotide anabolism 29    13 7.4E-12   
01.05.01    C-compound and carbohydrate utilization 510      18 1.4E-04
01.05.01.07.03 tetrahydrofolate-dependent C-1-transfer 14    6 5.8E-06   
11 TRANSCRIPTION 1036 126 9.4E-31     
11.02.01    rRNA synthesis 56 12 4.4E-06     
11.02.02    tRNA synthesis 39 9 3.8E-05     
11.04 RNA processing 394 89 9.4E-42     
11.04.01    rRNA processing 174 78 8.7E-62     
11.06 RNA modification 65 19 2.1E-11     
11.06.01    rRNA modification 17 9 1.0E-08     
12 PROTEIN SYNTHESIS 511 63 1.7E-14 103 7.6E-53   
12.01    ribosome biogenesis 343 49 8.5E-14 89 1.0E-54   
12.01.01 ribosomal proteins 277    88 1.8E-62   
14 PROTEIN FATE (folding, modification, destination)        
14.07.02    modification with sugar residues 70      8 4.1E-06
14.07.02.01 O-directed glycosylation 16      4 5.2E-05
16 PROTEIN WITH BINDING FUNCTION 1049 82 4.6E-08     
16.03    nucleic acid binding 346 47 2.0E-12     
16.03.03 RNA binding 194 31 2.8E-10     
20 CELLULAR TRANSPORT, TRANSPORT FACILITATION... 1038       
20.01.13    lipid transport 43      5 3.3E-05
MIPS_cat.    1 (120 genes) 2 & 3 (577 genes) 4, 5 & 6 (617 genes)
nr.    description nr of genesa nr of genesb p-value nr of genesb p-value nr of genesb p-value
01 METABOLISM 1531    193 4.3E-08 192 1.3E-05
01.05    C-compound and carbohydrate metabolism 510    89 2.6E-10 80 4.9E-06
01.05.01.01.01 sugar, glucoside, polyol and carboxylate catabolism 82      27 4.7E-09
01.06    lipid, fatty acid and isoprenoid metabolism 292      55 6.6E-07
01.06.01.07 isoprenoid metabolism 41      14 1.6E-05
01.06.01.07.11 tetracyclic and pentacyclic triterpenes biosynthesis 36      13 1.6E-05
02 ENERGY 360    112 5.1E-35 69 1.1E-08
02.10    tricarboxylic-acid pathway 31    11 4.7E-05 12 1.5E-05
02.11    electron transport & membrane-ass. energy conservation 54    30 4.2E-18   
02.13    Respiration 131    53 1.1E-22   
02.13.03 aerobic respiration 74    38 5.2E-21   
02.19    metabolism of energy reserves 53      16 2.4E-05
02.25    oxidation of fatty acids 9    6 3.5E-05   
02.45.15 energy generation (e.g. ATP synthase) 18      9 1.5E-05
11 TRANSCRIPTION        
11.02.03.04.01    transcriptional activator 42 7 1.2E-05     
14 PROTEIN FATE (folding, modific., destination) 1167      173 1.6E-08
14.07.11    protein processing (proteolytic) 92      24 4.1E-07
14.13    protein degradation 264      61 3.6E-11
14.13.01 cytoplasmic and nuclear protein degradation 194      48 4.2E-10
14.13.01.01 proteasomal degradation 134      33 2.8E-07
20 CELLULAR TRANSPORT, TRANSPORT FAC. 1028       
20.01.15 electron/hydrogen transport 76    24 2.3E-08   
20.09    transport routes 695      98 4.2E-05
32 CELL RESCUE, DEFENSE AND VIRULENCE 559    77 7.4E-05   
32.01    stress response 454    73 4.2E-07   
32.01.01 oxydative stress response 56    18 10E-06   
32.01.07 unfolded protein response (ER quality control) 74    16 7.6E-04   
42 BIOGENESIS OF CELL. COMPONENTS        
42.16    mitochondrion 170    38 9.0E-08 35 1.1E-05
  1. a: amount of genes in the genome belonging to the specified functional category
  2. b: amount of genes in the respective clusters or group of clusters belonging to the specified functional category