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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