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Table 2 Interferon-induced genes identified in large-scale microarray analyses of SLE PBMC

From: Microarray analysis of gene expression in lupus

   Response of PBMC to IFN-α/β (type I)/IFN-γ (type II) Expression in SLE compared with control PBMC
Gene Protein Reference: [4]* [4] [5] [3]§ [6]||
IFIT1 Interferon-induced protein with tetratricopeptide repeats-1 18.3   Up Up Up
OASL 2'-5'-oligoadenylate synthetase-like 16.3 Up Up   Up
LY6E Lymphocyte antigen 6 complex, locus E 14.9 Up Up Up Up
OAS2 2'-5'-oligoadenylate synthetase 12.7   Up   Up
OAS3 2'-5'-oligoadenylate synthetase NA NA   Up  
IFI44 Hepatitis C microtubular aggregate protein 10.7   Up Up  
MX1 Myxovirus resistance 1 9.8 Up Up Up  
G1P3 Interferon, alpha-inducible protein (IFI-6-16) 7.1 Up   Up  
PRKR Protein kinase, interferon-α-inducible double-stranded RNA-dependent 6.9 Up   Up  
IFIT4 Interferon-induced protein with tetratricopeptide repeats 4 6.8 Up Up Up  
PLSCR1 Phospholipid scramblase 1 6.6 Up Up Up  
C1ORF29 Hypothetical protein expressed in osteoblasts; similar to IFI44 6.1 Up Up Up  
HSXIAPAF1 XIAPassociated factor-1 6.1 Up Up Up  
G1P2 Interferon, alpha-inducible protein (IFI-15K) 5.9 Up Up   
Hs. 17518 (Cig5) Viperin 5.5   Up   
IRF7 Interferon regulatory factor 7 4.6   Up Up  
CD69 Early T-cell activation antigen 4.1 Up    
LGALS3BP Lectin, galactoside-binding, soluble, 3 binding protein 3.8 Up Up   
IL1RN Interleukin-1 receptor antagonist 3.5 Up    Up
APOBEC3B Phorbolin 1-like 2.0 Up Up Up  
RGS1 Regulator of G-protein signaling 1 1.8 Up    
AGRN Agrin > 71.2 (γ → < 0) Up Up   
EREG Epiregulin 1.3 (α/β and γ → < 0) Up    
THBS1 Thrombospondin 1 1.3 (α/β and γ → < 0) Up    
ETS1 v-ets erythroblastosis virus E26 oncogene homolog 1 1.2 (α/β and γ → < 0) Up    
ADAM9 A disintegrin and metalloproteinase domain 9 1.1 (α/β and γ → < 0) Up    
SERPING1 Serine (or cysteine) proteinase inhibitor (C1 inhibitor) 0.85 Up   Up  
USP20 Ubiquitin specific protease 20 0.25 (α/β and γ → < 0) Down    
MATK Megakaryocyte-specific tyrosine kinase < 0.13 (α/β → < 0) Down    
FCGR1A Fc fragment of IgG, high-affinity Ia receptor 0.08 Up   Up  
  1. The genes and corresponding proteins listed were identified as significantly differentially expressed in SLE and healthy control PBMC in the study by Baechler and colleagues [4], or were among the most commonly overexpressed transcripts among SLE PBMC in the study by Bennett and colleagues [5]. The significant overexpression of these genes in SLE compared with control PBMC in microarray data sets from Crow and colleagues [3] or Han and colleagues [6] is also noted. In addition, genes identified by Baechler and colleagues as both regulated by type I (IFN-α/β) or type II (IFN-γ) and differentially expressed by SLE PBMC are noted. A ratio of gene expression induced in healthy PBMC by IFN-α/β (1000 U/ml for 6 hours) compared with IFN-γ (1000 U/ml for 6 hours) for each gene was calculated by determining the net microarray score for each of four control samples studied by Baechler and colleagues (stimulated microarray score minus unstimulated microarray score) for both IFN-α/β and IFN-γ stimulation, determining the average of the four scores, and dividing the IFN-α/β score by the IFN-γ score for each gene. In some cases, scores for both IFN-α/β- and IFN-γ-induced gene expression were less than background [indicated as (α/β and γ → < 0)]. When the score for either IFN-α/β-induced or IFN-γ-induced gene expression was less than the background, the score for the lower value was replaced with a score of 50, to permit the calculation of an approximate ratio. Abbreviations: JCA, juvenile chronic arthritis; NA, not available; OA, osteoarthritis; RA, rheumatoid arthritis. * The microarray system used was an Affymetrix U95A GeneChip (Affymetrix, Santa Clara, CA); 4566 genes were analyzed. Four healthy donors of PBMC were studied. The microarray system used was an Affymetrix U95A GeneChip; 4566 genes were analyzed. The donors of PBMC studied were 48 with SLE and 42 healthy. The microarray system used was an Affymetrix U95AV2 GeneChip; about 4600 genes were analyzed. The donors of PBMC studied were 30 pediatric with SLE, 12 with JCA, and 9 healthy children. §The microarray system used was a proprietary microarray from Expression Diagnostics, Inc; 8143 oligonucleotides are represented. The donors of PBMC studied were 22 with SLE, 15 with RA, 8 with OA, 2 with JCA, and 9 healthy. ||The microarray system used was a Mergen ExpressChip DNA Microarray (Mergen, Ltd, San Leandro, CA); 3002 genes are represented. The donors of PBMC studied were 10 with SLE and 18 healthy. Identified as capicua homolog in some studies.