Table 2 Potential key candidate genes identified from the transcriptome.

From: Identification of candidate genes that specifically regulate subcutaneous and intramuscular fat deposition using transcriptomic and proteomic profiles in Dingyuan pigs

Gene name

log2FC of HBF/LBF

FDR of HBF/LBF

log2FC in HIMF/LIMF

FDR in HIMF/LIMF

Gene function

FASN

− 2.96

1.00E−06

0.48

0.676

Metabolic pathways, fatty acid metabolism, AMPK signaling pathway, insulin signaling pathway, fatty acid biosynthesis

CA3

− 2.26

4.72E−03

− 0.85

0.579

Metabolic pathways, nitrogen metabolism, cellular anatomical entity, cellular process, metabolic process, binding, intracellular

TKT

− 1.06

5.20E−04

0.21

0.978

Metabolic pathways, carbon metabolism, amino acid biosynthesis, pentose phosphate pathway, alpha-amino acid metabolic process, sulfur compound metabolic process,

KLF2

1.41

5.50E−05

0.16

0.991

White fat cell differentiation

ACAT1

− 1.02

7.10E−05

− 0.43

0.953

Reproductive structure development, sulfur amino acid biosynthetic process, metabolic pathways, valine, leucine, and isoleucine degradation, propanoate metabolism, carbon metabolism, pyruvate metabolism

ALDH1L1

− 2.36

8.61E−08

− 0.91

0.913

One carbon pool by folate, One Carbon Metabolism, Folate Metabolism

ECHDC1

− 1.43

5.01E−09

− 0.02

0.996

Metabolic pathways, propanoate metabolism, metabolic process, catalytic activity

ADHFE1

− 1.85

2.19E−08

− 0.51

0.928

Reproduction, alpha-amino acid metabolic process, sulfur compound metabolic process, reproductive structure development, regulation of muscle system process, citric acid cycle, respiratory electron transport, pyruvate metabolism

ACADSB

− 1.19

4.80E−05

− 0.29

0.960

Metabolic pathways, valine, leucine, and isoleucine degradation, fatty acid degradation, fatty acid metabolism

ALDH6A1

− 1.18

4.35E−03

− 0.79

0.542

Metabolic pathways, valine, leucine, and isoleucine degradation, propanoate metabolism, carbon metabolism, inositol phosphate metabolism, beta-alanine metabolism

AACS

− 2.28

2.28E−10

− 0.68

0.733

Metabolic pathways, valine, leucine, and isoleucine degradation, butanoate metabolism

SERPINE1

1.64

3.08E−03

− 0.99

0.772

Adipogenesis, blood clotting cascade, complement and coagulation cascades

PPARD

1.31

5.48E−04

− 1.19

0.238

Pathways in cancer, PPAR signaling pathway, acute myeloid leukemia, Wnt signaling pathway, ion binding, metal ion binding, small molecule metabolic process

UBD

1.02

1.18E−03

0.07

0.995

Proteasome binding, protein ubiquitination, positive regulation of apoptotic process

UCP2

1.45

2.75E−03

0.28

0.974

Anatomical structure morphogenesis, reproductive structure development, cardiac muscle tissue development, cell junction organization, muscle cell development

FBP1

− 1.78

4.80E−03

− 3.34

–

Negative regulation of glycolytic process, regulation of gluconeogenesis, fructose 6-phosphate metabolic process, negative regulation of cell growth

ACSS3

− 1.20

9.09E−03

− 0.74

0.628

Metabolic pathways, propanoate metabolism

PFKFB1

− 3.27

6.02E−06

0.90

0.269

Regulation of glycolysis by fructose 2,6-bisphosphate metabolism, metabolism, glycolysis, glucose metabolism, focal adhesion-PI3K-Akt-mTOR-signaling pathway, carbohydrate metabolism

GCDH

− 1.17

2.19E−08

− 0.20

0.989

Metabolic pathways, fatty acid degradation, lysine degradation, tryptophan metabolism

ACP5

2.07

7.52E−03

0.92

0.953

Metabolism, metabolism of water-soluble vitamins and cofactors, NAD phosphorylation and dephosphorylation

PRG4

3.62

5.26E−01

− 1.39

1.948

Phospholipase-C Pathway, ERK signaling, integrin pathway, MAPK signaling

LPL

1.00

2.14E−03

1.16

0.102

Fatty acid β-oxidation, adipogenesis, PPAR signaling pathway, lipoprotein metabolism, triacylglyceride synthesis

PRKAG3

− 2.73

7.80E−03

1.88

0.001

Longevity regulating pathway, AMPK signaling pathway, apelin signaling pathway, insulin signaling pathway, oxytocin signaling pathway, non-alcoholic fatty liver disease, tight junction

RETREG1

− 0.74

4.03E−01

− 2.72

–

nucleolus, endoplasmic reticulum, Golgi apparatus

PRKAG2

− 0.50

6.82E−02

− 2.57

0.004

Vitamin digestion and absorption, thermogenesis, lipid metabolism

SMPDL3A

0.21

8.69E−01

− 3.53

–

Vitamin digestion and absorption, sphingomyelin phosphodiesterase activity, sphingomyelin metabolic process, cellular lipid metabolic process, membrane lipid catabolic process, sphingolipid catabolic process, phospholipid catabolic process

IRS2

− 0.04

9.72E−01

− 1.79

3.0E−04

Adipogenesis genes, focal adhesion-PI3K-Akt-mTOR-signaling pathway, erythropoietin activates phosphoinositide-3-kinase, IL-13 signaling pathway, signaling by type 1 insulin-like growth factor 1 receptor

BDH1

− 0.06

9.75E−01

− 1.93

0.009

Vitamin digestion and absorption, butanoate metabolism, metabolic pathways, ketone body catabolism, lipid metabolism

PPARA

− 0.58

5.02E−01

− 1.59

0.001

Vitamin digestion and absorption, cAMP signaling pathway, Hepatitis C

GK

0.07

9.67E−01

− 1.99

0.004

Vitamin digestion and absorption, glycerolipid metabolism, metabolic pathways

LEP

0.72

3.29E−01

3.17

2.3E−04

AMP-activated protein kinase Signaling, adipocytokine signaling pathway, peptide hormone metabolism, cytokine-cytokine receptor interaction

  1. LBF low backfat thickness, HBF high backfat thickness, HIMF high intramuscular fat, LIMF low intramuscular fat, log2FC log2 fold change, FDR false discovery rate.
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