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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

From: Transcriptomic comparison of communally reared wild, domesticated and hybrid Atlantic salmon fry under stress and control conditions

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   
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