A comparison of gene transcription profiles of domesticated and wild Atlantic salmon (Salmo salar L.) at early life stages, reared under controlled conditions

Bicskei, Beatrix; Bron, James E; Glover, Kevin A; Taggart, John B

doi:10.1186/1471-2164-15-884

Table 2 Significantly differentially represented KEGG pathways (multiple testing corrected p ≤ 0.1) between wild and domesticated stocks in the two life stages, wild fish is considered as control

From: A comparison of gene transcription profiles of domesticated and wild Atlantic salmon (Salmo salar L.) at early life stages, reared under controlled conditions

	KEGG functional group	KEGG sub-group	KEGG pathway	Direction of perturbation	p-value	Set size
Sac fry	Cellular Processes	Cell growth and death	Oocyte meiosis	Up regulated	0.00212	15
	Environmental Information Processing	Signal transduction	Hippo signaling pathway	Up regulated	0.00128	15
	Environmental Information Processing	Signal transduction	Wnt signaling pathway	Up regulated	0.00053	20
	Genetic Information Processing	Folding, sorting and degradation	Protein processing in endoplasmic reticulum	Up regulated	0.00186	36
	Genetic Information Processing	Translation	Aminoacyl-tRNA biosynthesis	Up regulated	0.00734	13
	Genetic Information Processing	Translation	Ribosome	Up regulated	0.00016	50
	Genetic Information Processing	Translation	Ribosome biogenesis in eukaryotes	Up regulated	0.00024	31
	Genetic Information Processing	Translation	RNA transport	Up regulated	0.00002	39
	Cellular Processes	Transport and catabolism	Phagosome	Down regulated	0.00042	37
	Environmental Information Processing	Signal transduction	NF-kappa B signaling pathway	Down regulated	0.00093	25
	Environmental Information Processing	Signaling molecules and interaction	Cytokine-cytokine receptor interaction	Down regulated	≤0.00001	26
	Organismal Systems	Immune system	B cell receptor signaling pathway	Down regulated	0.00133	16
	Organismal Systems	Immune system	Chemokine signaling pathway	Down regulated	≤0.00001	38
	Organismal Systems	Immune system	Complement and coagulation cascades	Down regulated	0.00385	21
	Organismal Systems	Immune system	Fc epsilon RI signaling pathway	Down regulated	0.00778	16
	Organismal Systems	Immune system	Hematopoietic cell lineage	Down regulated	0.00007	14
	Organismal Systems	Nervous system	Glutamatergic synapse	Down regulated	0.00152	19
	Organismal Systems	Nervous system	Serotonergic synapse	Down regulated	0.00303	16
	Organismal Systems	Nervous system	Synaptic vesicle cycle	Down regulated	0.00171	18
	Metabolism	Lipid metabolism	Glycerophospholipid metabolism	Down regulated	0.00781	10
	Environmental Information Processing	Signal transduction	NF-kappa B signaling pathway	Two way perturbed	0.00116	25
	Environmental Information Processing	Signal transduction	TNF signaling pathway	Two way perturbed	0.00368	19
	Environmental Information Processing	Signaling molecules and interaction	Cytokine-cytokine receptor interaction	Two way perturbed	0.00001	26
	Environmental Information Processing	Signaling molecules and interaction	Neuroactive ligand-receptor interaction	Two way perturbed	0.00371	23
	Organismal Systems	Development	Osteoclast differentiation	Two way perturbed	0.00555	28
	Organismal Systems	Immune system	Chemokine signaling pathway	Two way perturbed	0.00343	38
	Organismal Systems	Immune system	NOD-like receptor signaling pathway	Two way perturbed	0.00416	14
	Organismal Systems	Immune system	Toll-like receptor signaling pathway	Two way perturbed	0.00240	19
	Metabolism	Lipid metabolism	Glycerophospholipid metabolism	Two way perturbed	0.00275	10
Feeding fry	Cellular Processes	Transport and catabolism	Peroxisome	Up regulated	0.00014	27
	Environmental Information Processing	Signaling molecules and interaction	ECM-receptor interaction	Up regulated	0.01210	12
	Organismal Systems	Circulatory system	Cardiac muscle contraction	Up regulated	0.00939	20
	Organismal Systems	Digestive system	Fat digestion and absorption	Up regulated	0.00047	16
	Organismal Systems	Digestive system	Pancreatic secretion	Up regulated	0.00062	17
	Organismal Systems	Digestive system	Protein digestion and absorption	Up regulated	0.00004	23
	Organismal Systems	Endocrine system	Adipocytokine signaling pathway	Up regulated	0.00435	15
	Organismal Systems	Endocrine system	Insulin signaling pathway	Up regulated	≤0.00001	19
	Organismal Systems	Endocrine system	PPAR signaling pathway	Up regulated	≤0.00001	29
	Metabolism	Amino acid metabolism	Arginine and proline metabolism	Up regulated	0.00014	17
	Metabolism	Amino acid metabolism	Glycine, serine and threonine metabolism	Up regulated	0.00029	17
	Metabolism	Carbohydrate metabolism	Glycolysis/Gluconeogenesis	Up regulated	0.00001	25
	Metabolism	Carbohydrate metabolism	Propanoate metabolism	Up regulated	0.00084	12
	Metabolism	Energy metabolism	Carbon fixation in photosynthetic organisms	Up regulated	0.00091	12
	Metabolism	Energy metabolism	Methane metabolism	Up regulated	0.00048	12
	Metabolism	Energy metabolism	Oxidative phosphorylation	Up regulated	0.00058	59
	Metabolism	Lipid metabolism	Biosynthesis of unsaturated fatty acids	Up regulated	0.00004	12
	Metabolism	Lipid metabolism	Fatty acid degradation	Up regulated	0.00056	16
	Metabolism	Lipid metabolism	Fatty acid elongation	Up regulated	0.00742	11
	Metabolism	Lipid metabolism	Glycerolipid metabolism	Up regulated	0.00429	15
	Environmental Information Processing	Signal transduction	Jak-STAT signaling pathway	Down Regulated	0.00005	16
	Environmental Information Processing	Signal transduction	NF-kappa B signaling pathway	Down Regulated	≤0.00001	28
	Environmental Information Processing	Signaling molecules and interaction	Cytokine-cytokine receptor interaction	Down Regulated	≤0.00001	38
	Environmental Information Processing	Signaling molecules and interaction	Neuroactive ligand-receptor interaction	Down Regulated	0.00122	22
	Organismal Systems	Immune system	Antigen processing and presentation	Down Regulated	0.00267	22
	Organismal Systems	Immune system	Chemokine signaling pathway	Down Regulated	≤0.00001	35
	Organismal Systems	Immune system	Cytosolic DNA-sensing pathway	Down Regulated	0.00799	10
	Organismal Systems	Immune system	Fc epsilon RI signaling pathway	Down Regulated	0.00130	12
	Organismal Systems	Immune system	Fc gamma R-mediated phagocytosis	Down Regulated	0.00407	17
	Organismal Systems	Immune system	Toll-like receptor signaling pathway	Down Regulated	0.00055	17
	Genetic Information Processing	Folding, sorting and degradation	Proteasome	Down Regulated	≤0.00001	25
	Environmental Information Processing	Signaling molecules and interaction	Cytokine-cytokine receptor interaction	Two way perturbed	≤0.00001	38

Set size is the number of genes included in the gene set test. Non-redundant pathways are shown in bold.

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ISSN: 1471-2164

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