Table 2.
Significantly differentially represented KEGG pathways (multiple testing corrected p ≤ 0.1) between wild and domesticated stocks in the two life stages, wild fish is considered as control
| KEGG functional group | KEGG sub-group | KEGG pathway | Direction of perturbation | p-value | Set size | |
|---|---|---|---|---|---|---|
| Sac fry | Cellular Processes | Cell growth and death | Oocyte meiosis | Up regulated | 0.00212 | 15 |
| Environmental Information Processing | Signal transduction | Hippo signaling pathway | Up regulated | 0.00128 | 15 | |
| Environmental Information Processing | Signal transduction | Wnt signaling pathway | Up regulated | 0.00053 | 20 | |
| Genetic Information Processing | Folding, sorting and degradation | Protein processing in endoplasmic reticulum | Up regulated | 0.00186 | 36 | |
| Genetic Information Processing | Translation | Aminoacyl-tRNA biosynthesis | Up regulated | 0.00734 | 13 | |
| Genetic Information Processing | Translation | Ribosome | Up regulated | 0.00016 | 50 | |
| Genetic Information Processing | Translation | Ribosome biogenesis in eukaryotes | Up regulated | 0.00024 | 31 | |
| Genetic Information Processing | Translation | RNA transport | Up regulated | 0.00002 | 39 | |
| Cellular Processes | Transport and catabolism | Phagosome | Down regulated | 0.00042 | 37 | |
| Environmental Information Processing | Signal transduction | NF-kappa B signaling pathway | Down regulated | 0.00093 | 25 | |
| Environmental Information Processing | Signaling molecules and interaction | Cytokine-cytokine receptor interaction | Down regulated | ≤0.00001 | 26 | |
| Organismal Systems | Immune system | B cell receptor signaling pathway | Down regulated | 0.00133 | 16 | |
| Organismal Systems | Immune system | Chemokine signaling pathway | Down regulated | ≤0.00001 | 38 | |
| Organismal Systems | Immune system | Complement and coagulation cascades | Down regulated | 0.00385 | 21 | |
| Organismal Systems | Immune system | Fc epsilon RI signaling pathway | Down regulated | 0.00778 | 16 | |
| Organismal Systems | Immune system | Hematopoietic cell lineage | Down regulated | 0.00007 | 14 | |
| Organismal Systems | Nervous system | Glutamatergic synapse | Down regulated | 0.00152 | 19 | |
| Organismal Systems | Nervous system | Serotonergic synapse | Down regulated | 0.00303 | 16 | |
| Organismal Systems | Nervous system | Synaptic vesicle cycle | Down regulated | 0.00171 | 18 | |
| Metabolism | Lipid metabolism | Glycerophospholipid metabolism | Down regulated | 0.00781 | 10 | |
| Environmental Information Processing | Signal transduction | NF-kappa B signaling pathway | Two way perturbed | 0.00116 | 25 | |
| Environmental Information Processing | Signal transduction | TNF signaling pathway | Two way perturbed | 0.00368 | 19 | |
| Environmental Information Processing | Signaling molecules and interaction | Cytokine-cytokine receptor interaction | Two way perturbed | 0.00001 | 26 | |
| Environmental Information Processing | Signaling molecules and interaction | Neuroactive ligand-receptor interaction | Two way perturbed | 0.00371 | 23 | |
| Organismal Systems | Development | Osteoclast differentiation | Two way perturbed | 0.00555 | 28 | |
| Organismal Systems | Immune system | Chemokine signaling pathway | Two way perturbed | 0.00343 | 38 | |
| Organismal Systems | Immune system | NOD-like receptor signaling pathway | Two way perturbed | 0.00416 | 14 | |
| Organismal Systems | Immune system | Toll-like receptor signaling pathway | Two way perturbed | 0.00240 | 19 | |
| Metabolism | Lipid metabolism | Glycerophospholipid metabolism | Two way perturbed | 0.00275 | 10 | |
| Feeding fry | Cellular Processes | Transport and catabolism | Peroxisome | Up regulated | 0.00014 | 27 |
| Environmental Information Processing | Signaling molecules and interaction | ECM-receptor interaction | Up regulated | 0.01210 | 12 | |
| Organismal Systems | Circulatory system | Cardiac muscle contraction | Up regulated | 0.00939 | 20 | |
| Organismal Systems | Digestive system | Fat digestion and absorption | Up regulated | 0.00047 | 16 | |
| Organismal Systems | Digestive system | Pancreatic secretion | Up regulated | 0.00062 | 17 | |
| Organismal Systems | Digestive system | Protein digestion and absorption | Up regulated | 0.00004 | 23 | |
| Organismal Systems | Endocrine system | Adipocytokine signaling pathway | Up regulated | 0.00435 | 15 | |
| Organismal Systems | Endocrine system | Insulin signaling pathway | Up regulated | ≤0.00001 | 19 | |
| Organismal Systems | Endocrine system | PPAR signaling pathway | Up regulated | ≤0.00001 | 29 | |
| Metabolism | Amino acid metabolism | Arginine and proline metabolism | Up regulated | 0.00014 | 17 | |
| Metabolism | Amino acid metabolism | Glycine, serine and threonine metabolism | Up regulated | 0.00029 | 17 | |
| Metabolism | Carbohydrate metabolism | Glycolysis/Gluconeogenesis | Up regulated | 0.00001 | 25 | |
| Metabolism | Carbohydrate metabolism | Propanoate metabolism | Up regulated | 0.00084 | 12 | |
| Metabolism | Energy metabolism | Carbon fixation in photosynthetic organisms | Up regulated | 0.00091 | 12 | |
| Metabolism | Energy metabolism | Methane metabolism | Up regulated | 0.00048 | 12 | |
| Metabolism | Energy metabolism | Oxidative phosphorylation | Up regulated | 0.00058 | 59 | |
| Metabolism | Lipid metabolism | Biosynthesis of unsaturated fatty acids | Up regulated | 0.00004 | 12 | |
| Metabolism | Lipid metabolism | Fatty acid degradation | Up regulated | 0.00056 | 16 | |
| Metabolism | Lipid metabolism | Fatty acid elongation | Up regulated | 0.00742 | 11 | |
| Metabolism | Lipid metabolism | Glycerolipid metabolism | Up regulated | 0.00429 | 15 | |
| Environmental Information Processing | Signal transduction | Jak-STAT signaling pathway | Down Regulated | 0.00005 | 16 | |
| Environmental Information Processing | Signal transduction | NF-kappa B signaling pathway | Down Regulated | ≤0.00001 | 28 | |
| Environmental Information Processing | Signaling molecules and interaction | Cytokine-cytokine receptor interaction | Down Regulated | ≤0.00001 | 38 | |
| Environmental Information Processing | Signaling molecules and interaction | Neuroactive ligand-receptor interaction | Down Regulated | 0.00122 | 22 | |
| Organismal Systems | Immune system | Antigen processing and presentation | Down Regulated | 0.00267 | 22 | |
| Organismal Systems | Immune system | Chemokine signaling pathway | Down Regulated | ≤0.00001 | 35 | |
| Organismal Systems | Immune system | Cytosolic DNA-sensing pathway | Down Regulated | 0.00799 | 10 | |
| Organismal Systems | Immune system | Fc epsilon RI signaling pathway | Down Regulated | 0.00130 | 12 | |
| Organismal Systems | Immune system | Fc gamma R-mediated phagocytosis | Down Regulated | 0.00407 | 17 | |
| Organismal Systems | Immune system | Toll-like receptor signaling pathway | Down Regulated | 0.00055 | 17 | |
| Genetic Information Processing | Folding, sorting and degradation | Proteasome | Down Regulated | ≤0.00001 | 25 | |
| Environmental Information Processing | Signaling molecules and interaction | Cytokine-cytokine receptor interaction | Two way perturbed | ≤0.00001 | 38 |
Set size is the number of genes included in the gene set test. Non-redundant pathways are shown in bold.