Skip to main content

Table 3 Differentially expressed genes related to the antigen processing and presentation pathways

From: RNA-seq liver transcriptome analysis reveals an activated MHC-I pathway and an inhibited MHC-II pathway at the early stage of vaccine immunization in zebrafish

Gene name

Accession number

Description

RPKM-C

RPKM-V

Fold-change

p-value

ciita

ENSDARG00000090851

MHC class II, transactivator

0.70

0.03

−26.80

5.54E-07

si:busm1-160c18.3

ENSDARG00000093706

Beta chain, MHC class II

2.04

0.36

−7.22

3.43E-04

mhc2dab

ENSDARG00000079105

MHC class II DAB gene

15.90

2.62

−7.22

2.16E-17

si:busm1-194e12.12

ENSDARG00000055447

Novel MHC II beta chain protein

6.12

1.70

−4.33

1.70E-06

lamp2

ENSDARG00000014914

Lysosomal membrane glycoprotein 2

3.47

1.11

−4.14

5.36E-03

cd74

ENSDARG00000036628

MHC, class II invariant chain, CD74 molecule,

34.87

10.77

−3.93

6.53E-12

ctsz

ENSDARG00000043081

Cathepsin Z

4.67

1.51

−3.77

8.36E-03

ctssb.1

ENSDARG00000074656

Cathepsin S, b.1

23.25

10.44

−2.59

4.24E-06

cd9a

ENSDARG00000005842

CD9 antigen

37.62

19.91

−2.34

5.21E-05

eif4a1b

ENSDARG00000003032

CD68 antigen variant

472.12

258.97

−2.33

1.94E-05

cd151l

ENSDARG00000068629

CD151 antigen, like

0.71

4.88

4.80

1.16E-03

psme3

ENSDARG00000012234

Proteasome activator complex subunit 3

8.68

19.69

2.02

6.74E-03

itm1

ENSDARG00000053832

Integral membrane protein 1(STT3)

121.55

311.95

2.03

6.23E-04

psme2

ENSDARG00000033144

Proteasome activator PA28 subunit 2

10.22

25.23

2.04

1.27E-03

pomp

ENSDARG00000032296

Proteasome maturation protein

12.60

31.84

2.13

2.01E-03

tapbpl

ENSDARG00000058351

TAP binding protein-like(TAPBPL)

5.75

15.38

2.18

1.09E-03

psme1

ENSDARG00000002165

Proteasome activator PA28 subunit 1

12.99

39.58

2.65

4.72E-05

canx

ENSDARG00000037488

Calnexin

49.15

167.03

2.85

3.71E-06

cd82b

ENSDARG00000026070

CD82 antigen,b

5.33

19.59

2.99

5.56E-07

si:ch211-287j19.6

ENSDARG00000001470

MHC class I ZE protein

4.96

18.39

3.09

1.63E-06

itfg1

ENSDARG00000075584

T-cell immunomodulatory protein

1.74

7.16

3.21

6.74E-07

hspa4a

ENSDARG00000004754

Heat shock protein 4a

5.42

18.17

3.28

9.21E-06

psma5

ENSDARG00000003526

Proteasome (prosome, macropain) subunit, alpha

1.90

7.52

3.60

9.48E-04

calr

ENSDARG00000043276

ER-resident chaperone calreticulin

29.97

131.43

3.72

4.47E-10

psmb3

ENSDARG00000013938

Proteasome (prosome, macropain) subunit, beta

13.34

60.15

3.80

3.27E-09

psmf1

ENSDARG00000022652

Proteasome (prosome, macropain) inhibitor

3.38

15.05

3.94

1.51E-06

psmg4

ENSDARG00000090191

Proteasome (prosome, macropain)

2.39

11.31

4.22

6.25E-04

hsp90a.2

ENSDARG00000024746

Heat shock protein HSP 90 kDa alpha 2

0.54

2.81

4.39

7.07E-05

psmc1b

ENSDARG00000043561

Proteasome (macropain) 26 S subunit

12.62

67.60

4.55

2.86E-15

hsp70

ENSDARG00000021924

Heat shock cognate 70 kDa protein

0.24

2.13

6.67

1.06E-05

cd63

ENSDARG00000025147

CD63 antigen

32.31

296.86

7.61

4.69E-20

cd276

ENSDARG00000003061

CD276 molecule

0.60

7.15

7.94

2.91E-08

cd97

ENSDARG00000089904

CD97 molecule

1.40

13.32

8.03

1.35E-31

hsp90b1

ENSDARG00000003570

Endoplasmin (grp94)

93.60

1118.80

10.06

2.85E-18

gata2a

ENSDARG00000059327

GATA-binding protein 2a

0.08

1.04

12.76

8.73E-03

ctsl1a

ENSDARG00000007836

Cathepsin L, 1 a

20.92

340.42

13.53

1.98E-43

dnajb11

ENSDARG00000015088

DnaJ (Hsp40) homolog, subfamily B

3.42

61.99

15.13

1.19E-32

  1. Identification of all differentially expressed genes was based on p<0.05. A p-value<0.05 indicated that the gene was significantly altered in WED-immunized fish with respect to mock-immunized fish. The absolute value of “Fold-change” is the magnitude of up- or down-regulation for each gene/homolog after WED immunization. Fold-change > 2 indicates up-regulation, and < −2 indicates down-regulation.
Back to article page

BMC Genomics

ISSN: 1471-2164

Contact us