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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

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 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   
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