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Table 3 Pathways found to be differentially expressed between control and stress conditions in reciprocal hybrids by both gage and romer packages. The direction of change shown describes the expression of the pathway under stress condition relative to control condition. 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 subgroup Pathway Genes W♀D♂ D♀W♂
gage romer gage romer
Cellular Processes 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
Environmental Information Processing Signal transduction ErbB signaling pathway 40    2D Down
HIF-1 signaling pathway 47    Up Up
MAPK signaling pathway 110    2D Up
Signaling molecules and interaction Neuroactive ligand-receptor interaction 112 2D Up Up/2D Up
Genetic Information Processing Folding, sorting and degradation Proteasome 40 Down Down/Mixed Down Down/Mixed
Replication and repair Base excision repair 28 Down Down/Mixed Down Down/Mixed
DNA replication 33 Down/2D Down/Mixed Down/2D Down/Mixed
Homologous recombination 20 Down Down/Mixed Down Down/Mixed
Mismatch repair 18 Down Down/Mixed Down/2D Down/Mixed
Nucleotide excision repair 35 Down Down/Mixed Down Down/Mixed
Transcription Spliceosome 109 Down Down/Mixed Down Down/Mixed
Translation Ribosome biogenesis in eukaryotes 64 Down Down/Mixed Down Down/Mixed
RNA transport 111 Down Down   
Metabolism Carbohydrate metabolism Citrate cycle (TCA cycle) 22 Up Up Up Up
Galactose metabolism 16 Up Up/Mixed   
Glycolysis / Gluconeogenesis 30 Up Up/Mixed Up Up/Mixed
Starch and sucrose metabolism 21    Up Up
Energy metabolism Carbon fixation in photosynthetic organisms 15    Up Up/Mixed
Oxidative phosphorylation 105 Up Up Up Up
Glycan biosynthesis and metabolism Glycosaminoglycan biosynthesis - heparan sulfate / heparin 11 2D Up   
Lipid metabolism Fatty acid degradation 24 Up Up Up Up
Glycerolipid metabolism 25 Up Up   
Glycerophospholipid metabolism 44    Up Up
Metabolism of cofactors and vitamins One carbon pool by folate 13    Down Down/Mixed
Nucleotide metabolism Purine metabolism 104 Down Down/Mixed Down Down/Mixed
Pyrimidine metabolism 73 Down Down/Mixed Down Down/Mixed
Organismal Systems Circulatory system Cardiac muscle contraction 41 Up Up/Mixed   
Vascular smooth muscle contraction 55 2D Up Up/2D Up
Digestive system Carbohydrate digestion and absorption 15 2D Up   
Fat digestion and absorption 19 Up Up Up Up
Gastric acid secretion 27    Up/2D Up
Pancreatic secretion 43    Up Up
Protein digestion and absorption 40    Up Up
Vitamin digestion and absorption 17    Up Up
Endocrine system Adipocytokine signaling pathway 35 2D Up Up/2D Up
Insulin secretion 37    Up/2D Up
Insulin signaling pathway 56    Up Up
PPAR signaling pathway 42 Up Up/Mixed Up Up/Mixed
Environmental adaptation Circadian rhythm 19    2D Up
Immune system T cell receptor signaling pathway 61    2D Down
Nervous system GABAergic synapse 38    Up Up
Glutamatergic synapse 50    2D Up
Long-term potentiation 28    2D Up
Retrograde endocannabinoid signaling 46    2D Up
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