Table 2 Pathways found to be differentially expressed between control and stress conditions in pure wild and domesticated stocks by both gage and romer packages. The direction of change shown describes the expression of the pathway in the stressed fish relative to the control state. The terms “2D” and “Mixed” are used to describe pathways in which genes showed bidirectional change. “Genes” refers to the number of genes included in the gene set test
KEGG group | KEGG sub-group | Pathway | Genes | Wild | Domesticated | ||
|---|---|---|---|---|---|---|---|
gage | romer | gage | romer | ||||
Cellular Processes | Cell communication | Gap junction | 39 | 2D | Down | ||
Cell growth and death | Cell cycle | 88 | Down | Down/Mixed | Down | Down/Mixed | |
Cell cycle – yeast | 54 | Down | Down/Mixed | Down | Down/Mixed | ||
Meiosis – yeast | 41 | Down | Down/Mixed | Down | Down/Mixed | ||
Transport and catabolism | Endocytosis | 105 | 2D | Up | |||
Environmental Information Processing | Signal transduction | Hippo signaling pathway – fly | 29 | 2D | Down | 2D | Down |
Signaling molecules and interaction | Cytokine-cytokine receptor interaction | 94 | 2D | Up | |||
Neuroactive ligand-receptor interaction | 112 | Up/2D | Up | ||||
Genetic Information Processing | Folding, sorting and degradation | Proteasome | 40 | Down | Down | Down | Down/Mixed |
Replication and repair | Base excision repair | 28 | Down | Down/Mixed | Down | Down/Mixed | |
DNA replication | 33 | Down | Down/Mixed | Down | Down/Mixed | ||
Fanconi anemia pathway | 35 | Down | Down/Mixed | ||||
Homologous recombination | 20 | Down | Down/Mixed | Down | Down | ||
Mismatch repair | 18 | Down | Down/Mixed | Down | Down/Mixed | ||
Nucleotide excision repair | 35 | Down | Down/Mixed | ||||
Transcription | Spliceosome | 109 | Down | Down | Down | Down | |
Translation | Ribosome biogenesis in eukaryotes | 64 | Down | Down/Mixed | Down | Down/Mixed | |
Metabolism | Carbohydrate metabolism | Glycolysis / Gluconeogenesis | 30 | Up | Up/Mixed | ||
Energy metabolism | Oxidative phosphorylation | 105 | Up | Up | Up | Up | |
Metabolism of cofactors and vitamins | Nicotinate and nicotinamide metabolism | 12 | Up | Up/Mixed | |||
Nucleotide metabolism | Purine metabolism | 104 | Down | Down/Mixed | |||
Pyrimidine metabolism | 73 | Down | Down/Mixed | Down | Down/Mixed | ||
Lipid metabolism | Fatty acid degradation | 24 | Up | Up | |||
Organismal Systems | Circulatory system | Cardiac muscle contraction | 41 | Up | Up | ||
Digestive system | Carbohydrate digestion and absorption | 15 | Up | Up | |||
Fat digestion and absorption | 19 | Up | Up/Mixed | Up | Up | ||
Gastric acid secretion | 27 | 2D | Up | ||||
Mineral absorption | 25 | Up | Up | ||||
Protein digestion and absorption | 40 | Up | Up | ||||
Vitamin digestion and absorption | 17 | Up | Up | ||||
Endocrine system | Adipocytokine signaling pathway | 35 | Up/2D | Up/Mixed | |||
Insulin secretion | 37 | 2D | Up | ||||
PPAR signaling pathway | 42 | Up | Up/Mixed | ||||
Excretory system | Proximal tubule bicarbonate reclamation | 11 | Up | Up | |||
Immune system | B cell receptor signaling pathway | 39 | 2D | Mixed | |||
Fc epsilon RI signaling pathway | 29 | 2D | Down | ||||
Natural killer cell mediated cytotoxicity | 40 | 2D | Down | ||||