Table 2 RNA-seq results of the top differentially expressed genes in the mid intestine between fish fed the SBM-based diet and FM-based diet.

From: Transcriptomic response to soybean meal-based diets as the first formulated feed in juvenile yellow perch (Perca flavescens)

Up-Regulated Genes

Gene Symbol

Log2(FC)

P-value

Cholesterol Biosynthetic Pathway

squalene monooxygenase

SQLE

2.67

0.004

farnesyl-diphosphate farnesyltransferase 1

FDFT1

2.53

0.005

methylsterol monooxygenase 1

MSMO1

2.42

0.002

cholesterol 7-alpha-monooxygenase

CYP7A1

2.05

0.008

3-hydroxy-3-methylglutaryl-coA synthase 1

HMGCS1

2.03

0.024

mevalonate diphosphate decarboxylase

MVD

1.89

0.012

hydroxymethylglutaryl-CoA reductase

HMGCR

2.14

0.004

lanosterol 14-alpha demethylase

CYP51A1

1.82

0.005

emopamil-binding protein

EBP

1.69

0.002

Lipid Transport and Metabolism

polyunsaturated fatty acid elongase

ELVOL5

1.98

0.045

long chain fatty acid elongase 6

ELVOL6

1.69

0.023

low-density lipoprotein receptor-related protein 2-like

LRP2

1.78

0.012

phthiocerol synthesis polyketide synthase type I

PPSD

1.71

0.044

proprotein convertase subtillisin/kexin type 9

PCKS9

1.60

0.001

Other Metabolic Processes

cathepsin B

CTSB

1.91

0.001

transcobalamin 2-like

TCO2

1.74

0.002

renin binding protein

RENBP

1.71

0.006

natterin 3-like

 NATT3

1.53

0.004

perilipin-3-like

PLIN3

1.52

0.021

Cellular Processes

dihydropyrimidinase related protein 5-like

DPY5

2.66

0.017

Eukaryotic translation initiation factor

EIF5

1.51

0.002

LaminA

LMNA

2.63

0.002

Immune Response

ubiquitin carboxyl-terminal hydrolase 10-like

USP10

2.98

0.004

carcinoembryonic antigen related cell adhesion molecule 1-like

CAECAM1

2.51

0.001

butyrophilin subfamily 2 member A2

BTN2A2

2.29

0.002

carcinoembryonic antigen related cell adhesion molecule 5-like

CAECAM5

1.68

0.017

NACHT, LRR and PYD domains containing protein 12 like

NLRP12

1.57

0.008

Down-Regulated Genes

Gene Symbol

Log2(FC)

P-value

Lipid/Cholesterol Regulation

mid-1 interacting protein 1-B like

M1IP1

−2.16

0.017

bile salt export pump-like

BSEP

−1.51

0.007

Cell Signaling

high choriolytic enzyme 1-like

HCEA

−3.51

0.022

C1q tumor necrosis factor related protein 3-like

C1QTNF3

−2.69

0.019

cytochrome P450 1A

CYP1A

−2.06

0.031

neurexophilin 2

NXPH2

−1.80

0.015

peroxisomal 2,4 -dienoyl CoA Reductase -like

PECR

−1.65

0.029

  1. All genes were found to be significantly different between treatments (p < 0.05), and expression was consistent among replicates within a treatment.
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