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Table 3 Relative expression of genes assayed by RT-qPCR

From: Effects of genotype and dietary fish oil replacement with vegetable oil on the intestinal transcriptome and proteome of Atlantic salmon (Salmo salar)

Genes VO/FO Lean/Fat
  Lean Fat FO VO
  Ratio p value Ratio p value Ratio p value Ratio p value
Microarray validation
Δ5fad (D) 1.72 ns 4.34 0.005 2.49 ns −1.01 ns
NADH1 (D) −1.03 ns −1.28 0.05 1.00 ns 1.24 ns
UCP2 (D) −1.10 ns 1.08 ns −1.10 ns −1.28 0.003
MTHFD1 (D) 1.20 ns −1.09 ns −1.08 ns 1.22 ns
PA2G4 (D) −1.27 ns −1.23 0.032 1.11 ns 1.1 ns
RP60S (D) −1.02 ns −1.69 0.023 1.13 ns 1.9 0.006
MYO (D) 1.77 0.034 1.22 ns −1.35 ns 1.08 ns
PCNA (D) −1.14 ns −1.27 ns 1.08 ns 1.20 ns
CYP1A (D+G) 1.71 0.004 1.81 0.023 −2.22 0.003 −2.38 0.001
ABCA1 (G) 1.24 ns 1.17 ns 1.21 ns 1.28 0.015
PSMB8 (G) −100.00 ns 1.87 0.033 −16.67 0.026 < −1000 0.000
TAGLN (G) 1.23 ns −1.02 ns −1.03 ns 1.22 ns
COL1A2 (G) 1.31 ns −1.06 ns 1.47 ns 2.06 0.001
LC-PUFA biosynthesis and regulation
Δ6fad_a 1.11 ns 2.96 0.008 1.76 ns −1.52 ns
elovl5a 1.08 ns 1.2 ns 1.03 ns −1.08 ns
elovl5b −1.19 ns 1.92 0.031 1.54 ns −1.47 ns
elovl2 1.2 ns 14.74 0.003 4.89 ns −2.50 ns
Fatty acid synthesis
FAS 1.49 0.010 1.20 ns 1.05 ns 1.31 ns
Fatty acid oxidation
ACO 1.18 ns 1.28 ns 1.19 ns 1.09 ns
CPT1 1.23 ns −1.09 ns −1.16 ns 1.15 ns
Regulation of lipid metabolism
PPARα 1.14 ns 1.38 ns 1.26 ns 1.04 ns
PPARβ 1.03 ns 1.03 ns −1.02 ns −1.02 ns
PPARγ 1.52 ns 1.60 0.036 1.21 ns 1.15 ns
Xenobiotic and oxidative stress
GST −1.30 ns 1.07 ns 1.21 ns −1.14 ns
MT-A −1.82 0.051* −1.05 ns −1.25 ns −2.13 0.007
CAT 1.57 0.036 1.26 ns −1.52 ns −1.22 ns
SOD −1.20 ns −1.04 ns 1.21 ns 1.04 ns
Apoptosis
CASP3B 1.22 0.045 1.22 ns −1.04 ns −1.04 ns
CASP6A/B 1.30 ns 1.37 ns −1.14 ns −1.20 ns
  1. fad: Fatty acyl desaturase (Δ5 and Δ6 activities); NADH1: NADH dehydrogenase subunit 1; UCP2: Uncoupling protein 2; elovl: MTHFD1: Methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like; PA2G4: Proliferation-associated 2G4b; RP60S: 60S acidic ribosomal protein; MYO: Myosin heavy chain; PCNA: Proliferating cell nuclear antigen; CYP1A: Cytochrome P4501A; ABCA1: ATP-binding cassette sub-family A member 1; PSMB8: Proteasome subunit beta type-8 precursor; TAGLN: Transgelin 2; COL1A2: Collagen type I alpha 2; elovl2: Elongase 2; FAS: Fatty acid synthase; ACO: Acyl-CoA oxidase; CPT1: Carnitine palmitoyltransferase I; PPARs; Peroxisome proliferator-activated receptors; GST: glutathione S-transferase; MT-A: Metallothionein A; CAT: catalase; SOD: superoxide dismutase; CASP; caspase.
  2. *Only marginally non-significant.
  3. Genes correspond to features significantly affected by either diet (D) or genotype (G) in the microarray analysis or involved in biological processes being analysed in further detail. Values are normalized (by cofilin-2 and elf-1 α) gene expression ratios between fish fed VO in relation to FO for each family group or of Lean fish in relation to the Fat group when fed either one of the diets. Values in bold are significantly different, at p<0.05 (REST 2008); ns - non-significant.