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Table 3
Differentially regulated genes (probe sets) in responders and nonresponders
Symbol	Accession number	Probe set	Function	J value	Direction^a	Significance^b

Transcription/regulation of transcription
TNFAIP3	AI738896	202643_s_at	TNFα-induced protein 3	1.1830	-	+
TNFAIP3	NM_006290	202644_s_at	TNFα-induced protein 3	0.9956	-	+
NFKBIA	AI078167	201502_s_at	NFκB enhancer in B-cell inhibitor alpha	0.4762	-	+
RUNX1	L21756	211620_x_at	Runt-related transcription factor 1	0.3940	+	+
JUN	BG491844	201464_x_at	c-jun proto-oncogene	0.1352	-	-
ZFP36L2	AI356398	201367_s_at	Zinc finger protein 36, C3H type-like 2	0.1308	-	+
SRRM2	AI655799	208610_s_at	Serine/arginine repetitive matrix 2	0.0081	+	-
ASCL1	AW950513	213768_s_at	Achaete-scute complex-like 1	0.0444	-	-
FOXO3A	AF041336	210655_s_at	Forkhead box O3A	0.0131	-	-
Immune response
IL1B	NM_000576	205067_at	IL-1β	0.9716	-	+
IL1B	M15330	39402_	IL-1β	0.9523	-	+
CCL4	NM_002984	204103_at	Chemokine (C-C motif) ligand 4	0.8002	-	+
CCL3	NM_002983	205114_s_at	Chemokine (C-C motif) ligand 3	0.4621	-	+
CXCR4	AF348491	211919_s_at	Chemokine (C-X-C motif) receptor 4	0.2589	-	-
CXCL2	M57731	209774_x_at	Chemokine (C-X-C motif) ligand 2	0.2532	-	+
LTF	NM_002343	202018_s_at	Lactotransferrin	0.1884	-	-
PBEF1	NM_005746	217739_s_at	Pre-B-cell colony-enhancing factor 1	0.0751	-	-
IGHA1	S55735	217022_s_at	Immunoglobulin heavy constant alpha 1	0.0475	-	-
IER3	NM_003897	201631_s_at	Immediate early response 3	0.0284	-	-
Receptors, cell surface antigens, cell adhesion
ADAM12	AU145357	215613_at	ADAM metallopeptidase domain 12 (meltrin alpha)	0.5538	-	+
ICAM1	AI608725	202637_s_at	Intercellular adhesion molecule 1 (CD54)	0.5399	-	-
SCN2B	U87555	210364_at	Sodium channel, voltage-gated, type II, beta	0.2294	+	+
Signal transduction
PDE4B	L20966	211302_s_at	Phosphodiesterase 4B, cAMP-specific	0.4374	-	+
RAPGEF1	NM_005312	204543_at	Rap guanine nucleotide-exchange factor 1	0.2890	-	+
MYO10	AI1561354	216222_s_at	Myosin X	0.2066	-	+
PTPRD	NM_002839	205712_at	Protein tyrosine phosphatase, receptor type, D	0.1822	+	+
SOCS1	AI056051	209999_x_at	Suppressor of cytokine signaling 1	0.1239	-	-
PDE4B	NM_002600	203708_at	Phosphodiesterase 4B, cAMP-specific	0.0593	-	+
Metabolism
LGALS13	NM_013268	220440_at	Lectin, galactose-binding, soluble, 13 (galectin 13)	0.5013	+	+
SNCA	BG260394	204466_s_at	Synuclein, alpha	0.0568	-	-
CHST3	AB017915	32094_at	Carbohydrate sulfotransferase 3	0.0366	-	+
Cellular and oxidative stress response
CROP	AW089673	208835_s_at	Cisplatin resistance-associated overexpressed protein	0.7500	+	+
PPP1R15A	NM_014330	202014_at	Protein phosphatase 1, regulatory (inhibitor) subunit 15A	0.6886	-	+
PPP1R15A	U83981	37028_at	Protein phosphatase 1, regulatory (inhibitor) subunit 15A	0.5939	-	-
DDIT4	M_019058	202887_s_at	DNA-damage-inducible transcript 4	0.2366	-	-
SOD2	W46388	215223_s_at	Superoxide dismutase 2, mitochondrial	0.0724	-	-
ADM	NM_001124	202912_at	Adrenomedullin	0.0459	-	+
Transport
ATP2A3	AF068220	207521_s_at	ATPase, Ca²⁺transporting, ubiquitous	0.227	-	-
CHRND	NM_000751	207024_at	Cholinergic receptor, nicotinic, delta	0.1977	-	+
Protein binding
PIGO	AC004472	214990_at	Phosphatidylinositol glycan, class O	0.5216	-	+
IBRDC3	W27419	36564_at	IBR domain containing 3	0.1194	-	+
EBP49	NM_001978	204505_s_at	Erythrocyte membrane protein band 4.9 (dematin)	0.0804	-	-
FBX07	NM_012179	201178_at	F-box protein 7	0.0080	-	-
Unknown
FSD1	NM_024333	219170_at	Fibronectin type III and SPRY domain containing 1	0.2935	-	+
HCG4P6	AF036973	215974_at	HLA complex group 4 pseudogene 6	0.1518	-	+
C20orf103	NM_013361	219463_at	Chromosome 20 open reading frame 103	0.0022	-	-

Genes were identified as differentially regulated using a modified t-statistic score, J (see Additional file 1), calculated using signal log ratios at t₁versus t₀considering 12 responders and seven nonresponders to etanercept therapy. ^aDirection denotes genes as stronger downregulated or lesser upregulated in responders compared with nonresponders (-), and vice versa (+). ^b+, significance approved by the resampling method with the modified t statistic on the significance level α = 0.05 (see Data processing and analysis section).
Koczan et al. Arthritis Research & Therapy 2008 10:R50 doi:10.1186/ar2419

Table 3