Table 7.
Enrichment of GO Biological Processes (GO-BP) by the genes differentially expressed in response to E2 or to Gen (analyses “E2” vs “Gen”). Significantly enriched biological processes (FDR < 0.05), identified by their ID and term description, are grouped into 12 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 group representation in Fig. 3 of the associated MS in JSBMB [1]. Functionally related groups are sorted by the highest enrichment score, calculated as [- Log2 (group FDR)]. The classification of each term as specifically enriched in response to the E2 or Gen treatments (or both), obtained by ClueGO cluster analysis, is also shown. For groups including terms enriched in more than one treatment, the classification of the leading term was adopted for the group.
| GOID | GOTerm | Term FDR | Group FDR | Enrichment Score | GOGroups | % Associated Genes | Nr. Genes | Treatment | %Genes Specific for E2 | %Genes Specific for Gen |
|---|---|---|---|---|---|---|---|---|---|---|
| GO:0043207 | Response to external biotic stimulus | 540.0E-12 | 100.0E-12 | 33.2 | 7 | 8.54 | 21.00 | Specific for Gen | 51.67 | 73.19 |
| GO:0051707 | response to other organism | 540.0E-12 | 100.0E-12 | 33.2 | 7 | 8.54 | 21.00 | Specific for Gen | 51.67 | 73.19 |
| GO:0009615 | response to virus | 28.0E-6 | 100.0E-12 | 33.2 | 7 | 12.96 | 7.00 | Specific for Gen | 50.61 | 63.26 |
| GO:0009617 | response to bacterium | 1.1E-3 | 100.0E-12 | 33.2 | 7 | 5.20 | 9.00 | Specific for Gen | 55.51 | 74.01 |
| GO:0043207 | Response to external biotic stimulus | 540.0E-12 | 8.9E-9 | 26.7 | 9 | 8.54 | 21.00 | Specific for Gen | 51.67 | 73.19 |
| GO:0051707 | response to other organism | 540.0E-12 | 8.9E-9 | 26.7 | 9 | 8.54 | 21.00 | Specific for Gen | 51.67 | 73.19 |
| GO:0051591 | response to cAMP | 36.0E-6 | 8.9E-9 | 26.7 | 9 | 75.00 | 3.00 | Specific for Gen | 45.51 | 68.26 |
| GO:0009617 | response to bacterium | 1.1E-3 | 8.9E-9 | 26.7 | 9 | 5.20 | 9.00 | Specific for Gen | 55.51 | 74.01 |
| GO:0046683 | response to organophosphorus | 1.8E-3 | 8.9E-9 | 26.7 | 9 | 20.00 | 3.00 | Specific for Gen | 45.51 | 68.26 |
| GO:0014074 | response to purine-containing compound | 1.8E-3 | 8.9E-9 | 26.7 | 9 | 20.00 | 3.00 | Specific for Gen | 45.51 | 68.26 |
| GO:0032496 | response to lipopolysaccharide | 2.0E-3 | 8.9E-9 | 26.7 | 9 | 8.33 | 5.00 | Specific for Gen | 49.63 | 66.17 |
| GO:0002237 | response to molecule of bacterial origin | 2.3E-3 | 8.9E-9 | 26.7 | 9 | 7.94 | 5.00 | Specific for Gen | 49.63 | 66.17 |
| GO:0042493 | response to drug | 10.0E-3 | 8.9E-9 | 26.7 | 9 | 9.38 | 3.00 | Specific for Gen | 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 Gen | 45.51 | 68.26 |
| GO:0016126 | Sterol biosynthetic process | 2.2E-9 | 1.3E-6 | 19.6 | 11 | 31.03 | 9.00 | Specific for Gen | 20.36 | 91.63 |
| GO:0006694 | steroid biosynthetic process | 3.0E-9 | 1.3E-6 | 19.6 | 11 | 19.30 | 11.00 | Specific for Gen | 17.00 | 93.49 |
| GO:0016125 | sterol metabolic process | 7.3E-9 | 1.3E-6 | 19.6 | 11 | 20.83 | 10.00 | Specific for Gen | 18.53 | 92.66 |
| GO:0008202 | steroid metabolic process | 7.7E-9 | 1.3E-6 | 19.6 | 11 | 14.63 | 12.00 | Specific for Gen | 15.69 | 94.16 |
| GO:1901617 | organic hydroxy compound biosynthetic process | 660.0E-9 | 1.3E-6 | 19.6 | 11 | 15.25 | 9.00 | Specific for Gen | 20.36 | 91.63 |
| GO:0008203 | cholesterol metabolic process | 2.0E-6 | 1.3E-6 | 19.6 | 11 | 20.59 | 7.00 | Specific for Gen | 25.30 | 88.56 |
| GO:1902652 | secondary alcohol metabolic process | 3.2E-6 | 1.3E-6 | 19.6 | 11 | 18.92 | 7.00 | Specific for Gen | 25.30 | 88.56 |
| GO:0006695 | cholesterol biosynthetic process | 8.7E-6 | 1.3E-6 | 19.6 | 11 | 31.25 | 5.00 | Specific for Gen | 17.96 | 89.82 |
| GO:1902653 | secondary alcohol biosynthetic process | 13.0E-6 | 1.3E-6 | 19.6 | 11 | 27.78 | 5.00 | Specific for Gen | 17.96 | 89.82 |
| GO:1901615 | organic hydroxy compound metabolic process | 33.0E-6 | 1.3E-6 | 19.6 | 11 | 7.69 | 10.00 | Specific for Gen | 18.53 | 92.66 |
| GO:0044283 | small molecule biosynthetic process | 60.0E-6 | 1.3E-6 | 19.6 | 11 | 5.85 | 12.00 | Specific for Gen | 29.87 | 89.62 |
| GO:0046165 | alcohol biosynthetic process | 100.0E-6 | 1.3E-6 | 19.6 | 11 | 17.86 | 5.00 | Specific for Gen | 17.96 | 89.82 |
| GO:0008610 | lipid biosynthetic process | 310.0E-6 | 1.3E-6 | 19.6 | 11 | 4.86 | 12.00 | Specific for Gen | 15.69 | 94.16 |
| GO:0006066 | alcohol metabolic process | 340.0E-6 | 1.3E-6 | 19.6 | 11 | 8.33 | 7.00 | Specific for Gen | 25.30 | 88.56 |
| GO:0016053 | organic acid biosynthetic process | 1.0E-3 | 1.3E-6 | 19.6 | 11 | 5.97 | 8.00 | Specific for Gen | 32.52 | 86.72 |
| GO:0046394 | carboxylic acid biosynthetic process | 1.0E-3 | 1.3E-6 | 19.6 | 11 | 5.97 | 8.00 | Specific for Gen | 32.52 | 86.72 |
| GO:1901607 | alpha-amino acid biosynthetic process | 1.0E-3 | 1.3E-6 | 19.6 | 11 | 10.42 | 5.00 | Specific for Gen | 33.08 | 82.71 |
| GO:0008652 | cellular amino acid biosynthetic process | 1.2E-3 | 1.3E-6 | 19.6 | 11 | 9.80 | 5.00 | Specific for Gen | 33.08 | 82.71 |
| GO:0031099 | Regeneration | 2.2E-3 | 1.3E-6 | 19.6 | 11 | 4.94 | 8.00 | Specific for Gen | 32.52 | 86.72 |
| GO:0006520 | cellular amino acid metabolic process | 5.6E-3 | 1.3E-6 | 19.6 | 11 | 4.15 | 8.00 | Specific for Gen | 22.58 | 90.31 |
| GO:0022600 | digestive system process | 6.0E-3 | 1.3E-6 | 19.6 | 11 | 12.00 | 3.00 | Specific for Gen | 26.42 | 79.25 |
| GO:1901605 | alpha-amino acid metabolic process | 6.3E-3 | 1.3E-6 | 19.6 | 11 | 5.08 | 6.00 | Specific for Gen | 28.72 | 86.17 |
| GO:0007586 | Digestion | 10.0E-3 | 1.3E-6 | 19.6 | 11 | 9.38 | 3.00 | Specific for Gen | 26.42 | 79.25 |
| GO:0072330 | monocarboxylic acid biosynthetic process | 14.0E-3 | 1.3E-6 | 19.6 | 11 | 5.97 | 4.00 | Specific for Gen | 38.69 | 77.37 |
| GO:0031331 | positive regulation of cellular catabolic process | 15.0E-3 | 1.3E-6 | 19.6 | 11 | 5.71 | 4.00 | Both treatments | 58.03 | 58.03 |
| GO:0009896 | positive regulation of catabolic process | 17.0E-3 | 1.3E-6 | 19.6 | 11 | 5.48 | 4.00 | Both treatments | 58.03 | 58.03 |
| GO:0097164 | ammonium ion metabolic process | 27.0E-3 | 1.3E-6 | 19.6 | 11 | 6.25 | 3.00 | Specific for Gen | 26.42 | 79.25 |
| GO:0015748 | organophosphate ester transport | 33.0E-3 | 1.3E-6 | 19.6 | 11 | 5.77 | 3.00 | Specific for Gen | 26.42 | 79.25 |
| GO:0006633 | fatty acid biosynthetic process | 33.0E-3 | 1.3E-6 | 19.6 | 11 | 5.77 | 3.00 | Specific for Gen | 26.42 | 79.25 |
| GO:0001878 | Response to yeast | 3.4E-6 | 4.8E-6 | 17.7 | 4 | 25.00 | 6.00 | Specific for Gen | 43.08 | 71.80 |
| GO:0009620 | response to fungus | 9.5E-6 | 4.8E-6 | 17.7 | 4 | 20.69 | 6.00 | Specific for Gen | 43.08 | 71.80 |
| GO:0031099 | Regeneration | 2.2E-3 | 350.0E-6 | 11.5 | 8 | 4.94 | 8.00 | Specific for Gen | 32.52 | 86.72 |
| GO:0042060 | wound healing | 2.8E-3 | 350.0E-6 | 11.5 | 8 | 4.68 | 8.00 | Specific for Gen | 52.30 | 73.22 |
| GO:0022600 | digestive system process | 6.0E-3 | 350.0E-6 | 11.5 | 8 | 12.00 | 3.00 | Specific for Gen | 26.42 | 79.25 |
| GO:0007586 | Digestion | 10.0E-3 | 350.0E-6 | 11.5 | 8 | 9.38 | 3.00 | Specific for Gen | 26.42 | 79.25 |
| GO:0042246 | tissue regeneration | 41.0E-3 | 350.0E-6 | 11.5 | 8 | 4.08 | 4.00 | Specific for Gen | 38.69 | 77.37 |
| GO:0007599 | Hemostasis | 43.0E-3 | 350.0E-6 | 11.5 | 8 | 5.08 | 3.00 | Specific for E2 | 68.26 | 45.51 |
| GO:0007596 | blood coagulation | 43.0E-3 | 350.0E-6 | 11.5 | 8 | 5.08 | 3.00 | Specific for E2 | 68.26 | 45.51 |
| GO:0050817 | Coagulation | 48.0E-3 | 350.0E-6 | 11.5 | 8 | 4.84 | 3.00 | Specific for E2 | 68.26 | 45.51 |
| GO:0006979 | Response to oxidative stress | 3.1E-3 | 3.9E-3 | 8.0 | 1 | 7.25 | 5.00 | Both treatments | 53.89 | 53.89 |
| GO:0031589 | cell-substrate adhesion | 8.6E-3 | 10.0E-3 | 6.6 | 5 | 7.02 | 4.00 | Specific for E2 | 64.60 | 43.07 |
| GO:0007160 | cell-matrix adhesion | 30.0E-3 | 10.0E-3 | 6.6 | 5 | 6.00 | 3.00 | Specific for E2 | 79.25 | 26.42 |
| GO:0006730 | One-carbon metabolic process | 13.0E-3 | 13.0E-3 | 6.3 | 0 | 8.57 | 3.00 | Specific for Gen | 0.00 | 100.00 |
| GO:0051241 | negative regulation of multicellular organismal process | 12.0E-3 | 14.0E-3 | 6.2 | 3 | 4.32 | 6.00 | Specific for Gen | 51.88 | 77.82 |
| GO:0001945 | Lymph vessel development | 35.0E-3 | 35.0E-3 | 4.8 | 2 | 5.56 | 3.00 | Specific for E2 | 68.26 | 45.51 |
| GO:0000188 | Inactivation of MAPK activity | 260.0E-6 | 39.0E-3 | 4.7 | 10 | 22.22 | 4.00 | Specific for Gen | 53.43 | 71.24 |
| GO:0043407 | negative regulation of MAP kinase activity | 420.0E-6 | 39.0E-3 | 4.7 | 10 | 19.05 | 4.00 | Specific for Gen | 53.43 | 71.24 |
| GO:0043409 | negative regulation of MAPK cascade | 1.1E-3 | 39.0E-3 | 4.7 | 10 | 14.29 | 4.00 | Specific for Gen | 53.43 | 71.24 |
| GO:0043405 | regulation of MAP kinase activity | 1.5E-3 | 39.0E-3 | 4.7 | 10 | 7.32 | 6.00 | Both treatments | 64.85 | 64.85 |
| GO:0071901 | negative regulation of protein serine/threonine kinase activity | 1.5E-3 | 39.0E-3 | 4.7 | 10 | 12.50 | 4.00 | Specific for Gen | 53.43 | 71.24 |
| GO:0033673 | negative regulation of kinase activity | 2.1E-3 | 39.0E-3 | 4.7 | 10 | 6.67 | 6.00 | Both treatments | 64.85 | 64.85 |
| GO:0006469 | negative regulation of protein kinase activity | 2.1E-3 | 39.0E-3 | 4.7 | 10 | 6.74 | 6.00 | Both treatments | 64.85 | 64.85 |
| GO:0051348 | negative regulation of transferase activity | 2.6E-3 | 39.0E-3 | 4.7 | 10 | 6.25 | 6.00 | Both treatments | 64.85 | 64.85 |
| GO:0001933 | negative regulation of protein phosphorylation | 2.9E-3 | 39.0E-3 | 4.7 | 10 | 6.12 | 6.00 | Both treatments | 64.85 | 64.85 |
| GO:0042326 | negative regulation of phosphorylation | 3.0E-3 | 39.0E-3 | 4.7 | 10 | 6.00 | 6.00 | Both treatments | 64.85 | 64.85 |
| GO:1902532 | negative regulation of intracellular signal transduction | 7.0E-3 | 39.0E-3 | 4.7 | 10 | 4.96 | 6.00 | Both treatments | 64.85 | 64.85 |
| GO:0071900 | regulation of protein serine/threonine kinase activity | 7.1E-3 | 39.0E-3 | 4.7 | 10 | 4.92 | 6.00 | Both treatments | 64.85 | 64.85 |
| GO:0001706 | endoderm formation | 14.0E-3 | 39.0E-3 | 4.7 | 10 | 8.11 | 3.00 | Specific for Gen | 45.51 | 68.26 |
| GO:0001704 | formation of primary germ layer | 17.0E-3 | 39.0E-3 | 4.7 | 10 | 5.48 | 4.00 | Specific for Gen | 53.43 | 71.24 |
| GO:0007492 | endoderm development | 49.0E-3 | 39.0E-3 | 4.7 | 10 | 4.76 | 3.00 | Specific for Gen | 45.51 | 68.26 |
| GO:0042541 | Hemoglobin biosynthetic process | 1.3E-3 | 62.0E-3 | 4.0 | 6 | 23.08 | 3.00 | Specific for Gen | 26.42 | 79.25 |
| GO:0020027 | hemoglobin metabolic process | 1.5E-3 | 62.0E-3 | 4.0 | 6 | 21.43 | 3.00 | Specific for Gen | 26.42 | 79.25 |
| GO:0055076 | transition metal ion homeostasis | 48.0E-3 | 62.0E-3 | 4.0 | 6 | 4.84 | 3.00 | Specific for Gen | 26.42 | 79.25 |