Table 1 Pathways found to be differentially expressed between wild and domesticated stocks under control and stress conditions by both gage and romer packages. The direction of change shown describes the expression of the pathway in the domesticated fish relative to wild counterparts. 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 | Control | Stress | ||
|---|---|---|---|---|---|---|---|
gage | romer | gage | romer | ||||
Cellular Processes | Cell communication | Focal adhesion | 98 | 2D | Down | 2D | Down |
Gap junction | 39 | 2D | Down | ||||
Cell growth and death | Cell cycle – yeast | 54 | Up | Up | Up | Up | |
Transport and catabolism | Phagosome | 76 | Down | Down/Mixed | Down | Down/Mixed | |
Endocytosis | 105 | Down/2D | Down | Down/2D | Down | ||
Peroxisome | 54 | Up | Up | Up | Up | ||
Environmental Information Processing | Membrane transport | ABC transporters | 27 | Up | Mixed | ||
Signal transduction | MAPK signaling pathway | 110 | 2D | Down | 2D | Down | |
NF-kappa B signaling pathway | 64 | 2D | Down | ||||
Jak-STAT signaling pathway | 56 | 2D | Down | ||||
Calcium signaling pathway | 72 | 2D | Down | 2D | Down | ||
PI3K-Akt signaling pathway | 149 | 2D | Down/Mixed | Down/2D | Down | ||
VEGF signaling pathway | 28 | 2D | Down | ||||
Signaling molecules and interaction | Cell adhesion molecules (CAMs) | 64 | 2D | Down/Mixed | 2D | Down | |
Neuroactive ligand-receptor interaction | 112 | Down/2D | Down | ||||
Cytokine-cytokine receptor interaction | 94 | Down/2D | Down | 2D | Down | ||
Genetic Information Processing | Replication and repair | DNA replication | 33 | Up | Up | ||
Transcription | RNA polymerase | 27 | Up | Up | Up | Up | |
Spliceosome | 109 | Up | Up | ||||
Translation | Ribosome biogenesis in eukaryotes | 64 | Up | Up | Up | Up/Mixed | |
RNA transport | 111 | Up | Up | Up | Up/Mixed | ||
Ribosome | 118 | Up | Up/Mixed | Up | Up/Mixed | ||
Metabolism | Amino acid metabolism | Arginine and proline metabolism | 36 | Up | Up | ||
Carbohydrate metabolism | Amino sugar & nucleotide sugar metabolism | 35 | Up | Up/Mixed | Up | Up/Mixed | |
Galactose metabolism | 16 | Up | Up/Mixed | Up | Up/Mixed | ||
Fructose and mannose metabolism | 19 | Up | Up/Mixed | Up | Up/Mixed | ||
Glycolysis / Gluconeogenesis | 30 | Up | Up/Mixed | ||||
Lipid metabolism | Sphingolipid metabolism | 21 | Up | Up | Up | Up | |
Biosynthesis of unsaturated fatty acids | 15 | Up | Up/Mixed | Up | Up/Mixed | ||
Glycerolipid metabolism | 25 | Up | Up/Mixed | ||||
Primary bile acid biosynthesis | 12 | Up | Up/Mixed | Up | Up/Mixed | ||
Nucleotide metabolism | Pyrimidine metabolism | 73 | Up | Up/Mixed | Up | Up | |
Xenobiotics biodegradation and metabolism | Drug metabolism - cytochrome P450 | 11 | Down | Down/Mixed | Down/2D | Down/Mixed | |
Organismal Systems | Circulatory system | Vascular smooth muscle contraction | 55 | 2D | Down | Down/2D | Down |
Development | Osteoclast differentiation | 69 | 2D | Down | 2D | Down | |
Axon guidance | 52 | Down/2D | Down | ||||
Digestive system | Protein digestion and absorption | 40 | 2D | Mixed | |||
Vitamin digestion and absorption | 17 | 2D | Up/Mixed | ||||
Mineral absorption | 25 | Up | Up/Mixed | ||||
Fat digestion and absorption | 19 | Up | Up/Mixed | Up | Up/Mixed | ||
Bile secretion | 39 | Up/2D | Up/Mixed | Up/2D | Up | ||
Salivary secretion | 32 | Down/2D | Down | ||||
Endocrine system | Ovarian steroidogenesis | 22 | 2D | Down | 2D | Down | |
Thyroid hormone synthesis | 33 | 2D | Up/Mixed | ||||
PPAR signaling pathway | 42 | Up | Up | ||||
Insulin secretion | 37 | 2D | Down | ||||
Environmental adaptation | Circadian entrainment | 45 | 2D | Down | Down/2D | Down | |
Immune system | T cell receptor signaling pathway | 61 | 2D | Down | |||
Fc epsilon RI signaling pathway | 29 | 2D | Down | 2D | Down/Mixed | ||
B cell receptor signaling pathway | 39 | 2D | Down | Down/2D | Down | ||
Complement and coagulation cascades | 56 | Down | Down/Mixed | Down | Down/Mixed | ||
Hematopoietic cell lineage | 38 | Down/2D | Down/Mixed | Down | Down | ||
Chemokine signaling pathway | 88 | Down/2D | Down/Mixed | Down/2D | Down/Mixed | ||
Natural killer cell mediated cytotoxicity | 40 | Down/2D | Down/Mixed | Down/2D | Down | ||
Nervous system | Glutamatergic synapse | 50 | 2D | Down | Down/2D | Down | |
Synaptic vesicle cycle | 35 | Down | Down | ||||
Serotonergic synapse | 49 | Down | Down | Down | Down | ||
Retrograde endocannabinoid signaling | 46 | 2D | Down | ||||
Sensory system | Phototransduction | 14 | Down | Down | |||