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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.
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BMC Genomics

ISSN: 1471-2164

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