Genome-wide expression profiles of subchondral bone in osteoarthritis

Chou, Ching-Heng; Wu, Chia-Chun; Song, I-Wen; Chuang, Hui-Ping; Lu, Liang-Suei; Chang, Jen-Huei; Kuo, San-Yuan; Lee, Chian-Her; Wu, Jer-Yuarn; Chen, Yuan-Tsong; Kraus, Virginia Byers; Lee, Ming Ta Michael

doi:10.1186/ar4380

Arthritis Research & Therapy

Table 3 Genes representative of gene clusters associated with osteoarthritis

From: Genome-wide expression profiles of subchondral bone in osteoarthritis

Functional annotation (number of genes, P value)^a	Representative genes				Fold-change (MT vs. LT)
	Accession number	Gene symbol	Gene name	P value^b	OA (microarray)	Non-OA (microarray)	OA (qRT-PCR)
Abnormal morphology of bone	NM_004370	COL12A1	Collagen, type XII, alpha 1	6.55 × 10^–08	2.26	1.01	1.76
(42 genes, P = 1.5 × 10^–6)	NM_000594	TNF	Tumor necrosis factor	1.17 × 10^–08	−3.17	−1.45	−3.42*
Abnormal morphology of collagen fibrils	NM_000093	COL5A1	Collagen, type V, alpha 1	2.63 × 10^–08	2.90	1.35	6.40*
(7 genes, P = 1.68 × 10^–6)	NM_000393	COL5A2	Collagen, type V, alpha 2	2.34 × 10^–10	3.12	1.40	3.18
Adiposity (24 genes, P <10^–7)	NM_003394	WNT10B	Wingless-type MMTV integration site Family, member 10B	9.76 × 10^–09	2.05	−1.08	NA
	NM_001279	CIDEA	Cell death-inducing DFFA-like effector a	2.74 × 10^–09	−6.26	−1.71	NA
Bone mineral density	NM_025237	SOST	Sclerostin	2.59 × 10^–04	2.51	1.44	4.77*
(21 genes, P = 1.1 × 10^–5)	NM_005357	LIPE	Lipase, hormone-sensitive	4.46 × 10^–09	−8.71	−1.73	−4.21*
Angiogenesis	NM_004673	ANGPTL1	Angiopoietin-like 1	2.55 × 10^–06	2.16	1.02	NA
(69 genes, P <10^–7)	NM_002982	CCL2	Chemokine (C–C motif) ligand 2	3.08 × 10^–05	−3.76	−1.31	−4.87*
Osteoarthritis	NM_001851	COL9A1	Collagen, type IX, alpha 1	1.42 × 10^–06	2.19	−1.05	2.35
(23 genes, P <10^–7)	NM_001463	FRZB	Frizzled-related protein	1.36 × 10^–10	−3.69	1.38	−7.72*
Proliferation of cells	NM_001004439	ITGA11	integrin, alpha 11	4.05 × 10^–10	2.31	−1.03	NA
(303 genes, P <10^–7)	NM_021077	NMB	Neuromedin B	1.14 × 10^–06	−3.00	−1.36	NA
	NM_004490	GRB14	Growth factor receptor-bound protein 14	3.38 × 10^–12	−3.20	−1.18	NA
	NM_006763	BTG2	BTG family, member 2	9.11 × 10^–08	−3.67	−1.31	NA
Quantity of connective tissue	NM_003474	ADAM12	ADAM metallopeptidase domain 12	1.86 × 10^–10	2.30	1.10	1.93
(48 genes, P <10^–7)	NM_022094	CIDEC	Cell death-inducing DFFA-like effector c	2.08 × 10^–07	−6.09	−1.63	NA
Differentiation of cells	NM_054034	FN1	Fibronectin 1	1.44 × 10^–07	2.19	1.38	2.10*
(175 genes, P <10^–7)	NM_016619	PLAC8	Placenta-specific 8	1.01 × 10^–08	−2.28	1.14	NA
Cell movement	NM_000094	COL7A1	Collagen, type VII, alpha 1	2.25 × 10^–09	2.28	−1.00	3.81*
(176 genes, P <10^–7)	NM_012193	FZD4	Frizzled family receptor 4	3.62 × 10^–10	−3.02	−1.37	4.93*
Necrosis	NM_080838	WISP1	WNT1 inducible signaling pathway protein 1	3.79 × 10^–08	2.50	1.09	NA
(218 genes, P <10^–7)	NM_004797	ADIPOQ	Adiponectin, C1Q and collagen domain containing	1.71 × 10^–07	−6.63	−1.69	10.51*
Mineralization of cells	NM_001719	BMP7	Bone morphogenetic protein 7	1.65 × 10^–09	2.50	1.34	2.26**
(14 genes, P = 3 × 10^–6)	NM_015424	CHRDL2	Chordin-like 2	1.40 × 10^–04	−4.04	1.38	−15.71*

LT, lateral tibial; MT, medial tibial; NA, not analyzed; OA, osteoarthritis. ^aNumber of genes associated with the particular ingenuity pathway and differentially expressed in MT versus LT regions of OA samples by microarray analysis; P value calculated by Fisher’s exact test. ^bAdjusted P value for microarray corrected for multiple testing by the Benjamini–Hochberg method. *P <0.001 and **P <0.05 for quantitative reverse-transcription polymerase chain reaction (qRT-PCR); P <0.05 was considered significant comparing OA MT versus OA LT. P values determined by two-tailed unpaired Student’s t test.

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