Table 3

Differentially expressed genes related to the antigen processing and presentation pathways
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

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.

Yang et al.

Yang et al. BMC Genomics 2012 13:319   doi:10.1186/1471-2164-13-319

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