Gene expression profiling in murine autoimmune arthritis during the initiation and progression of joint inflammation

Adarichev, Vyacheslav A; Vermes, Csaba; Hanyecz, Anita; Mikecz, Katalin; Bremer, Eric G; Glant, Tibor T

doi:10.1186/ar1472

Table 2 Array-based expression values of upregulated or downregulated genes in pre-inflamed joint

From: Gene expression profiling in murine autoimmune arthritis during the initiation and progression of joint inflammation

Affy ID	Description	Gene	Mean AN expression	AN presence call	Mean PA expression	PA presence call	Fold	Cluster
161968_f_at	Chemokine (CC motif) receptor 5	Ccr5	1	A	57.1	P	57.1	D
95349_g_at	Chemokine (CXC motif) ligand 1	Cxcl1	1	A	55.9	P	55.9	D
104750_at	Interferon-γ inducible protein	Ifi47	0.69	A	15.69	P	22.7	D
130509_at	Membrane-spanning 4-domains member A6C	Ms4a6c	1.17	A	10.27	P	8.78	D
93106_i_at	T-cell receptor beta, variable 13	Tcrbv13	1.86	A	10.34	P	5.55	A
98474_r_at	Tumor necrosis factor-α induced protein 6	Tnfaip6	3.61	A	19.97	P	5.54	D
94761_at	Chemokine (CC motif) ligand 7	Ccl7	24.47	A	115.33	P	4.71	D
101578_f_at	Actin, β, cytoplasmic	Actg	188.33	P	859.16	P	4.56	A
102736_at	Chemokine (CC motif) ligand 2	Ccl2	29.89	P	125.48	P	4.20	D
95121_at	Polymerase (DNA-directed) ε 4 p12	Pole4	8.95	P	26.13	P	2.92	C
93397_at	Chemokine (CC) receptor 2	Ccr2	93.67	P	259.21	P	2.77	D
102906_at	T cell-specific GTPase	Tgtp	24.27	A	66.03	P	2.72	D
97322_at	Membrane-spanning 4-domains member A6B	Ms4a6b	9.43	A	25.16	P	2.67	D
93514_at	Myosin, light polypeptide 3	Myl3	29.28	A	77.42	P	2.64	A
103089_at	CD48 antigen	Cd48	34.17	A	85.82	P	2.51	C
103507_at	EGF-like hormone receptor-like sequence 1	Emr1	59.04	A	145.95	P	2.47	D
96764_at	Interferon-inducible GTPase	Ifigtp	66.38	A	157.88	P	2.38	D
102326_at	Neutrophil cytosolic factor 2	Ncf2	23.67	P	55.88	P	2.36	D
104388_at	Chemokine (CC motif) ligand 9	Ccl9	246.56	P	568.47	P	2.31	D
93321_at	Interferon-activated gene 203	Ifi203	43.58	P	99.27	P	2.28	C
94085_at	Proteoglycan, secretory granule	Prg	329.68	P	747.2	P	2.27	D
92762_at	C-type lectin, superfamily member 6	Clecsf6	35.73	A	80.64	P	2.26	D
93136_at	Dermatan sulphate proteoglycan 3	Dspg3	30.23	A	67.77	P	2.24	B
101753_s_at	P lysozyme structural	Lzps	635.78	P	1398.72	P	2.20	D
94939_at	CD53 antigen	Cd53	112.16	P	243.17	P	2.17	D
94958_at	RIKEN cDNA 1110013L07 gene	1110013L07Rik	24.91	A	53.7	P	2.16	A
162066_f_at	Rho interacting protein 3	Rip3	19.15	A	40.54	P	2.12	A
93039_at	RIKEN cDNA 1190003P12 gene	1190003P12Rik	36.44	P	77.03	P	2.11	A
101048_at	Protein tyrosine phosphatase, receptor type, C	Ptprc	138.7	A	289.19	P	2.09	D
92217_s_at	Glycoprotein 49 B	Gp49b	72.11	P	148.01	P	2.05	D
93869_s_at	Hematopoietic-specific A1-d protein	Bcl2a1a	49.43	A	100.11	P	2.03	D
103989_at	RIKEN cDNA 4432417F03 gene	4432417F03Rik	35.66	A	72.18	P	2.02	B
160611_at	Cytochrome P450 polypeptide 4v3	Cyp4v3	82	P	164.59	P	2.01	B
162107_r_at	Tissue inhibitor of metalloproteinase 1	Timp1	9.64	P	4.39	A	-2.20	E
164493_i_at	Makorin, ring finger protein, 1	Mkrn1	8.23	P	3.21	A	-2.56	F
167637_i_at	RIKEN cDNA 4833424O15 gene	4833424O15Rik	8.19	P	2.64	A	-3.11	F
167950_r_at	Terf1 (TRF1)-interacting nuclear factor 2	Tinf2	8.82	P	1.65	P	-5.35	E

Affy ID, unique Affymetrix probe set identifier. Description, gene description. Gene, gene abbreviation. Mean AN expression, average expression value in basal experimental condition of clinically normal paws of naive severe combined immunodeficient mice without cell transfer. Mean PA expression, average expression value in pre-arthritic joints. Presence call, average presence call for gene in AN or PA experimental condition: P, transcript was actually present in the majority of samples; A, transcript was actually absent in the majority of samples. Fold, fold change in gene expression in PA joint compared with AN basal expression. Cluster, cluster designation from Fig. 5. Difference in expression was significant by Mann–Whitney U-test, P < 0.05. Differential expression for listed genes was either greater than twofold overexpression or less than twofold downregulation (negative values). Genes that were differentially expressed in both pre-inflamed paws and in vitro-stimulated lymphocytes used for cell transfer are shown in bold type.

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