Table 2

Differentially expressed genes in RASFsn-stimulated chondrocytes (FC ≥ 1,5; FC ≤ -1,5; GCOS)

Functional annotation: gene title (gene symbol)

Accession no.

Chondrocyte mean fold change in expression (GCOS analysis)

Chondrocyte mean signal intensity (GCOS analysis)


RASFsn versus NDSFsn stimulation

RASFsn stimulation

NDSFsn stimulation

No stimulation


Inflammatory/catabolic mediators

Catalase (CAT)

NM_001752.1

-1.7

672.85

1,221.90

1,386.65

Chemokine (C-C motif) ligand 5 (RANTES)

NM_002985.1

4.1

103.40

25.20

18.95

Chemokine orphan receptor 1 (CMKOR1)

AI817041

2.2

609.45

322.55

89.50

Glutathione peroxidase 3 (GPX3)

AW149846

-1.5

1,083.25

1,617.75

669.90

Interleukin-1β (IL-1β)

M15330

2.2

91.80

34.10

36.45

Interleukin-6 (IL-6)

NM_000600.1

2.6

10,058.00

4,907.15

56.25

Nuclear factor-κB associated gene (NF-κB1)

NM_003998.1

1.5

472.80

312.10

176.75

Nuclear factor-κB associated gene (NF-κB2)

BC002844.1

2.3

125.75

48.25

41.50

Prostaglandin E synthase (PGES)

NM_004878.1

1.9

1,308.70

596.10

123.10

TNF-α-inducible protein 2 (TNFAIP2)

NM_006291.1

2.6

337.65

109.90

98.90

Tumor necrosis factor receptor (TNFRSF1B)

NM_001066.1

2.3

439.20

197.70

67.10

ECM degradation

Matrix metalloproteinase 10 (MMP10)

NM_002425.1

2.7

587.60

233.90

20.05

Matrix metalloproteinase 12 (MMP12)

NM_002426.1

5.2

161.40

25.90

18.00

ECM formation

Collagen, type I, α1 (COL1A1)

NM_000088.1

-2.3

472.15

1,182.40

6,603.50

Collagen, type V, α1 (COL5A1)

N30339

-1.9

143.80

296.95

862.60

Collagen, type X, α1 (COL10A1)

X98568

-4.6

36.50

163.90

5.00

Collagen type XI, α1 (COL11A1)

J04177

-1.7

565.80

982.25

1,146.10

Testican-1

NM_004598

-1.8

543.80

1,384.10

2,311.00


Expression levels of rheumatoid arthritis-relevant genes that failed to reach the twofold regulation criteria for both GCOS and RMA statistical analyses are shown. Expression for all listed genes showed a reproducible regulation as determined by GCOS analysis. Genes were functionally categorized into inflammatory/catabolic mediators and genes involved in the degradation and formation of extracellular matrix (ECM), and are listed with accession number, mean fold change in expression (GCOS) and mean signal intensity (GCOS). Mean signal intensity of unstimulated chondrocytes is listed for the determination of baseline expression. The expression was not reproducibly changed for MMPs and collagens that are not listed in this table.

ECM, extracellular matrix; GCOS, GeneChip Operating Software; NDSFsn, supernatant of synovial fibroblast cell line derived from a normal donor; RASFsn, supernatant of synovial fibroblast cell line derived from a patient with rheumatoid arthritis; RMA, Robust Multi-array Analysis; TNFRSF1B, tumor necrosis factor receptor superfamily, member 1B.

Andreas et al. Arthritis Research & Therapy 2008 10:R9   doi:10.1186/ar2358

Open Data