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Table 4 Genes differentially expressed in DA versus E3 rats 8 days after pristane injection

From: Differential gene expression in pristane-induced arthritis susceptible DA versus resistant E3 rats

    Affymetrix    
Accession no. Gene ID Significance Pooled Individual Taqman Custom-made FACS
Upregulated        
   X56596 MHC class I antigen RT1.B-1 β-chain (MhcII) S I (47.4) I (43.4);
P < 0.0001
ND I (2.8);
P < 0.1
I (1.9);
P < 0.03
   U24441 Metalloproteinase 9 (Mmp9) T I (5) I (1.5);
P < 0.001
I (1.9);
P < 0.08
NC ND
   S81478 CL100 protein tyrosine phosphatase (Ptpn16) T I (2.4) NC* ND I (1.6);
P < 0.02
ND
Downregulated        
   L07399 (Hybridoma 56R-7) immunoglobulin rearranged
γ-chain variable (Ig γ)
S D (-6.4) NC* ND D (-2.0);
P < 0.02
ND
   L07401 (Hybridoma 57R-1) immunoglobulin rearranged
γ-chain variable (Ig γ)
S D (-62.4) NC* D (-2.1);
P < 0.03
NC ND
   M14434 Immunoglobulin active κ-chain VJC region
from immunocytoma IR2 (Ig κ)
S D (-34.7) NC* ND D (-1.9);
P < 0.003
ND
   X00923 IgE heavy chain (Ig ε) S D (-28) NC* ND D (-2.0);
P < 0.05
ND
   S81289 IgM κ-chain variable (Ig κ) S D (-9.3) NC* ND D (-2.5);
P < 0.0003
ND
   M15402 Immunoglobulin active κ-chain VJ region
from immunocytoma IR162 (Ig κ)
S D (-3.9) NC* ND D (-3.0);
P < 0.006
ND
   nm_013121 CD28 (Cd28) S NC NC* ND D (-2.2);
P < 0.01
D (-9.8);
P < 0.03
   S69206 Mast cell protease 1 (Mcpt1) S D (-4.7) NC* ND D (-2.1);
P < 0.002
ND
   AB010635 Carboxylesterase precursor (Ces2) S D (-4.1) NC* ND D (-2.5) ;
P < 0.003
ND
   D25290 K-cadherin (Cdh6) S D (-4.1) NC* ND D (-1.7) ;
P < 0.01
ND
   X70871 Cyclin G1 (Ccng1) S D (-9.6) D (-4.8);
P < 0.001
D NC ND
   AJ011608 DNA polymerase α-subunit IV (Primase) S D (-3.3) D (-2.6);
P < 0.001
D (-3.5);
P < 0.03
NC ND
   L12025 Tumour-associated glycoprotein E4 (Tage) T D (-3.1) NC* ND D (-1.8);
P < 0.1
ND
  1. To be regarded as differentially expressed a gene must be differentially expressed in two biological samples analyzed by a minimum of two independent methods. Differential expression values in bold text are statistically significant by that particular method. Genes significantly differentially expressed by a minimum of two independent methods are denoted 'S'. Another subset of genes showed a strong tendency toward differential expression; these are denoted 'T'. FACS, fluorescence activated cell sorting; NC, no change; ND, not determined. *These genes were not included among the 30 genes with highest probability of differential expression (t-test P < 0.002). This gene was only detectable in the E3 rat. For these genes, no statistically significant differential expression could be shown.