Table 9.
Enrichment of GO Biological Processes by the genes differentially expressed after 1 day or 5 days (Analyses “1d” vs “5d”). Significantly enriched biological processes (FDR < 0.05), identified by their ID and term description, are grouped according to 11 functionally related networks (GO group) obtained by ClueGO analysis. Each group is named after its most significant term (lowest FDR), highlighted in bold, which was chosen for GOTerm representation in Fig. 3 of the associated MS in JSBMB [1]. Functionally related groups are sorted by highest enrichment score, calculated as [- Log2 (group FDR)]. The classification of each term as specifically enriched in the responses after 1 day or 5 days (or both), obtained by ClueGO cluster analysis, is also shown. For groups including terms enriched in more than one list the classification of the leading term was adopted for the whole group.
| GOID | GOTerm | Term FDR | Group FDR | Enrichment Score | GOGroups | % Associated Genes | Nr. Genes | Time | %Genes Specific for 1d | %Genes Specific for 5d |
|---|---|---|---|---|---|---|---|---|---|---|
| GO:0043207 | Response to external biotic stimulus | 490.0E-12 | 100.0E-12 | 33.2 | 7 | 8.54 | 21.00 | Specific for 5 days | 36.49 | 72.99 |
| GO:0051707 | response to other organism | 490.0E-12 | 100.0E-12 | 33.2 | 7 | 8.54 | 21.00 | Specific for 5 days | 36.49 | 72.99 |
| GO:0009615 | response to virus | 26.0E-6 | 100.0E-12 | 33.2 | 7 | 12.96 | 7.00 | Specific for 5 days | 14.29 | 85.71 |
| GO:0009617 | response to bacterium | 1.0E-3 | 100.0E-12 | 33.2 | 7 | 5.20 | 9.00 | Specific for 5 days | 39.30 | 78.60 |
| GO:0043207 | Response to external biotic stimulus | 490.0E-12 | 8.9E-9 | 26.7 | 9 | 8.54 | 21.00 | Specific for 5 days | 36.49 | 72.99 |
| GO:0051707 | response to other organism | 490.0E-12 | 8.9E-9 | 26.7 | 9 | 8.54 | 21.00 | Specific for 5 days | 36.49 | 72.99 |
| GO:0051591 | response to cAMP | 33.0E-6 | 8.9E-9 | 26.7 | 9 | 75.00 | 3.00 | Specific for 5 days | 45.51 | 68.26 |
| GO:0009617 | response to bacterium | 1.0E-3 | 8.9E-9 | 26.7 | 9 | 5.20 | 9.00 | Specific for 5 days | 39.30 | 78.60 |
| GO:0046683 | response to organophosphorus | 1.7E-3 | 8.9E-9 | 26.7 | 9 | 20.00 | 3.00 | Specific for 5 days | 45.51 | 68.26 |
| GO:0014074 | response to purine-containing compound | 1.7E-3 | 8.9E-9 | 26.7 | 9 | 20.00 | 3.00 | Specific for 5 days | 45.51 | 68.26 |
| GO:0032496 | response to lipopolysaccharide | 1.9E-3 | 8.9E-9 | 26.7 | 9 | 8.33 | 5.00 | Specific for 5 days | 33.08 | 82.71 |
| GO:0002237 | response to molecule of bacterial origin | 2.2E-3 | 8.9E-9 | 26.7 | 9 | 7.94 | 5.00 | Specific for 5 days | 33.08 | 82.71 |
| GO:0042493 | response to drug | 10.0E-3 | 8.9E-9 | 26.7 | 9 | 9.38 | 3.00 | Specific for 5 days | 45.51 | 68.26 |
| GO:0009612 | response to mechanical stimulus | 23.0E-3 | 8.9E-9 | 26.7 | 9 | 6.67 | 3.00 | Specific for 5 days | 45.51 | 68.26 |
| GO:0016126 | Sterol biosynthetic process | 2.0E-9 | 76.0E-9 | 23.6 | 11 | 31.03 | 9.00 | Specific for 1 day | 84.82 | 21.21 |
| GO:0006694 | steroid biosynthetic process | 2.8E-9 | 76.0E-9 | 23.6 | 11 | 19.30 | 11.00 | Specific for 1 day | 78.95 | 26.32 |
| GO:0016125 | sterol metabolic process | 6.6E-9 | 76.0E-9 | 23.6 | 11 | 20.83 | 10.00 | Specific for 1 day | 86.42 | 19.21 |
| GO:0008202 | steroid metabolic process | 7.0E-9 | 76.0E-9 | 23.6 | 11 | 14.63 | 12.00 | Specific for 1 day | 80.73 | 24.22 |
| GO:1901617 | organic hydroxy compound biosynthetic process | 600.0E-9 | 76.0E-9 | 23.6 | 11 | 15.25 | 9.00 | Specific for 1 day | 84.82 | 21.21 |
| GO:0008203 | cholesterol metabolic process | 1.8E-6 | 76.0E-9 | 23.6 | 11 | 20.59 | 7.00 | Specific for 1 day | 80.21 | 26.74 |
| GO:1902652 | secondary alcohol metabolic process | 2.9E-6 | 76.0E-9 | 23.6 | 11 | 18.92 | 7.00 | Specific for 1 day | 80.21 | 26.74 |
| GO:0006695 | cholesterol biosynthetic process | 7.9E-6 | 76.0E-9 | 23.6 | 11 | 31.25 | 5.00 | Specific for 1 day | 89.82 | 17.96 |
| GO:1902653 | secondary alcohol biosynthetic process | 12.0E-6 | 76.0E-9 | 23.6 | 11 | 27.78 | 5.00 | Specific for 1 day | 89.82 | 17.96 |
| GO:1901615 | organic hydroxy compound metabolic process | 30.0E-6 | 76.0E-9 | 23.6 | 11 | 7.69 | 10.00 | Specific for 1 day | 86.42 | 19.21 |
| GO:0044283 | small molecule biosynthetic process | 54.0E-6 | 76.0E-9 | 23.6 | 11 | 5.85 | 12.00 | Specific for 1 day | 68.82 | 45.88 |
| GO:0046165 | alcohol biosynthetic process | 92.0E-6 | 76.0E-9 | 23.6 | 11 | 17.86 | 5.00 | Specific for 1 day | 89.82 | 17.96 |
| GO:0006066 | alcohol metabolic process | 330.0E-6 | 76.0E-9 | 23.6 | 11 | 8.33 | 7.00 | Specific for 1 day | 80.21 | 26.74 |
| GO:0016053 | organic acid biosynthetic process | 990.0E-6 | 76.0E-9 | 23.6 | 11 | 5.97 | 8.00 | Specific for 5 days | 54.20 | 65.04 |
| GO:0046394 | carboxylic acid biosynthetic process | 990.0E-6 | 76.0E-9 | 23.6 | 11 | 5.97 | 8.00 | Specific for 5 days | 54.20 | 65.04 |
| GO:1901607 | alpha-amino acid biosynthetic process | 1.0E-3 | 76.0E-9 | 23.6 | 11 | 10.42 | 5.00 | Specific for 5 days | 49.63 | 66.17 |
| GO:0008652 | cellular amino acid biosynthetic process | 1.1E-3 | 76.0E-9 | 23.6 | 11 | 9.80 | 5.00 | Specific for 5 days | 49.63 | 66.17 |
| GO:0072330 | monocarboxylic acid biosynthetic process | 14.0E-3 | 76.0E-9 | 23.6 | 11 | 5.97 | 4.00 | Both times | 58.03 | 58.03 |
| GO:0031331 | positive regulation of cellular catabolic process | 16.0E-3 | 76.0E-9 | 23.6 | 11 | 5.71 | 4.00 | Specific for 5 days | 43.07 | 64.60 |
| GO:0009896 | positive regulation of catabolic process | 17.0E-3 | 76.0E-9 | 23.6 | 11 | 5.48 | 4.00 | Specific for 5 days | 43.07 | 64.60 |
| GO:0097164 | ammonium ion metabolic process | 27.0E-3 | 76.0E-9 | 23.6 | 11 | 6.25 | 3.00 | Specific for 1 day | 79.25 | 26.42 |
| GO:0001878 | Response to yeast | 3.1E-6 | 4.8E-6 | 17.7 | 5 | 25.00 | 6.00 | Both times | 50.00 | 50.00 |
| GO:0009620 | response to fungus | 8.6E-6 | 4.8E-6 | 17.7 | 5 | 20.69 | 6.00 | Both times | 50.00 | 50.00 |
| GO:0031099 | Regeneration | 2.1E-3 | 150.0E-6 | 12.7 | 8 | 4.94 | 8.00 | Specific for 1 day | 75.88 | 43.36 |
| GO:0042060 | wound healing | 2.7E-3 | 150.0E-6 | 12.7 | 8 | 4.68 | 8.00 | Specific for 1 day | 73.22 | 52.30 |
| GO:0042246 | tissue regeneration | 42.0E-3 | 150.0E-6 | 12.7 | 8 | 4.08 | 4.00 | Specific for 1 day | 77.37 | 38.69 |
| GO:0007599 | hemostasis | 44.0E-3 | 150.0E-6 | 12.7 | 8 | 5.08 | 3.00 | Specific for 5 days | 45.51 | 68.26 |
| GO:0007596 | blood coagulation | 44.0E-3 | 150.0E-6 | 12.7 | 8 | 5.08 | 3.00 | Specific for 5 days | 45.51 | 68.26 |
| GO:0050817 | coagulation | 49.0E-3 | 150.0E-6 | 12.7 | 8 | 4.84 | 3.00 | Specific for 5 days | 45.51 | 68.26 |
| GO:0006979 | Response to oxidative stress | 2.9E-3 | 3.9E-3 | 8.0 | 0 | 7.25 | 5.00 | Specific for 1 day | 60.00 | 40.00 |
| GO:0031589 | Cell-substrate adhesion | 8.6E-3 | 10.0E-3 | 6.6 | 3 | 7.02 | 4.00 | Specific for 5 days | 43.07 | 64.60 |
| GO:0009266 | Response to temperature stimulus | 15.0E-3 | 19.0E-3 | 5.7 | 2 | 7.89 | 3.00 | Specific for 1 day | 100.00 | 0.00 |
| GO:0000188 | Inactivation of MAPK activity | 230.0E-6 | 29.0E-3 | 5.1 | 10 | 22.22 | 4.00 | Specific for 5 days | 38.69 | 77.37 |
| GO:0043407 | negative regulation of MAP kinase activity | 400.0E-6 | 29.0E-3 | 5.1 | 10 | 19.05 | 4.00 | Specific for 5 days | 38.69 | 77.37 |
| GO:0043409 | negative regulation of MAPK cascade | 1.0E-3 | 29.0E-3 | 5.1 | 10 | 14.29 | 4.00 | Specific for 5 days | 38.69 | 77.37 |
| GO:0043405 | regulation of MAP kinase activity | 1.4E-3 | 29.0E-3 | 5.1 | 10 | 7.32 | 6.00 | Specific for 5 days | 28.72 | 86.17 |
| GO:0071901 | negative regulation of protein serine/threonine kinase activity | 1.4E-3 | 29.0E-3 | 5.1 | 10 | 12.50 | 4.00 | Specific for 5 days | 38.69 | 77.37 |
| GO:0033673 | negative regulation of kinase activity | 1.9E-3 | 29.0E-3 | 5.1 | 10 | 6.67 | 6.00 | Specific for 5 days | 54.36 | 67.96 |
| GO:0006469 | negative regulation of protein kinase activity | 1.9E-3 | 29.0E-3 | 5.1 | 10 | 6.74 | 6.00 | Specific for 5 days | 54.36 | 67.96 |
| GO:0051348 | negative regulation of transferase activity | 2.5E-3 | 29.0E-3 | 5.1 | 10 | 6.25 | 6.00 | Specific for 5 days | 54.36 | 67.96 |
| GO:0001933 | negative regulation of protein phosphorylation | 2.7E-3 | 29.0E-3 | 5.1 | 10 | 6.12 | 6.00 | Specific for 5 days | 54.36 | 67.96 |
| GO:0042326 | negative regulation of phosphorylation | 2.8E-3 | 29.0E-3 | 5.1 | 10 | 6.00 | 6.00 | Specific for 5 days | 54.36 | 67.96 |
| GO:1902532 | negative regulation of intracellular signal transduction | 7.0E-3 | 29.0E-3 | 5.1 | 10 | 4.96 | 6.00 | Specific for 5 days | 54.36 | 67.96 |
| GO:0071900 | regulation of protein serine/threonine kinase activity | 7.1E-3 | 29.0E-3 | 5.1 | 10 | 4.92 | 6.00 | Specific for 5 days | 28.72 | 86.17 |
| GO:0001706 | endoderm formation | 15.0E-3 | 29.0E-3 | 5.1 | 10 | 8.11 | 3.00 | Specific for 5 days | 26.42 | 79.25 |
| GO:0001704 | formation of primary germ layer | 17.0E-3 | 29.0E-3 | 5.1 | 10 | 5.48 | 4.00 | Specific for 5 days | 21.53 | 86.14 |
| GO:0001945 | Lymph vessel development | 37.0E-3 | 39.0E-3 | 4.7 | 4 | 5.56 | 3.00 | Specific for 1 day | 68.26 | 45.51 |
| GO:0009142 | Nucleoside triphosphate biosynthetic process | 44.0E-3 | 44.0E-3 | 4.5 | 1 | 5.08 | 3.00 | Specific for 5 days | 0.00 | 100.00 |
| GO:0042541 | Hemoglobin biosynthetic process | 1.2E-3 | 62.0E-3 | 4.0 | 6 | 23.08 | 3.00 | Specific for 5 days | 26.42 | 79.25 |
| GO:0020027 | hemoglobin metabolic process | 1.4E-3 | 62.0E-3 | 4.0 | 6 | 21.43 | 3.00 | Specific for 5 days | 26.42 | 79.25 |
| GO:0055076 | transition metal ion homeostasis | 49.0E-3 | 62.0E-3 | 4.0 | 6 | 4.84 | 3.00 | Specific for 5 days | 26.42 | 79.25 |