Table 6

NP vs AC microarray comparison

Gene description

Gene symbol

AC mean

AF mean

NP mean

Fold change (NP/AC)


brain abundant, membrane attached signal protein 1

BASP1

0.02

57.19

384.21

16167.90

keratin 18

KRT18

0.01

0.04

94.10

15990.45

Tenomodulin

TNMD

0.01

241.03

102.36

15087.56

TNF, alpha-induced protein 6

TNFAIP6

0.01

304.98

121.88

8205.96

keratin 8

KRT8

0.09

0.39

714.79

7607.92

hypothetical protein BC012029

LOC152573

0.05

0.18

230.02

4635.12

TNF, alpha-induced protein 6

TNFAIP6

0.19

3649.85

508.71

2648.51

SH3 domain binding glutamic acid-rich protein

SH3BGR

0.08

20.83

172.70

2230.52

cadherin 2, type 1, N-cadherin (neuronal)

CDH2

0.09

0.22

180.47

1941.17

chordin

CHRD

0.03

1.29

57.29

1671.45

Rat sarcoma (ras) homolog gene family, member B

RHOB

0.24

0.04

383.01

1627.81

homeobox B8

HOXB8

0.08

9.11

119.75

1591.12

Rho GTPase activating protein 27

ARHGAP27

0.08

0.72

89.24

1072.84

forkhead box F1

FOXF1

0.43

703.54

457.76

1054.86

plakophilin 2

PKP2

0.13

0.48

77.71

603.25

homeobox B6

HOXB6

0.11

58.21

61.73

580.12

adaptor-related protein complex 2, mu 1 subunit

AP2M1

0.55

350.92

305.70

557.26

transketolase-like 1

TKTL1

0.89

4.59

478.18

536.27

cytochrome b-245, alpha polypeptide

CYBA

0.16

0.77

83.63

513.67

phosphatidylethanolamine-binding protein 4

PEBP4

0.84

113.44

429.31

511.40

forkhead box F2

FOXF2

0.60

416.30

283.89

470.91

Kruppel-like factor 6

KLF6

0.13

0.03

55.84

444.91

optineurin

OPTN

0.22

0.36

88.35

407.25

aquaporin 1 (Colton blood group)

AQP1

0.42

5.55

144.13

346.12

RAB3B, member RAS oncogene family

RAB3B

0.18

0.27

58.47

333.33

similar to sushi domain containing 2

SUSD2

1.05

34.26

300.30

286.96

sclerostin domain containing 1

SOSTDC1

0.28

0.53

79.27

286.23

CD36 molecule (thrombospondin receptor)

CD36

0.27

96.74

71.61

262.65

capping protein (actin filament), gelsolin-like

CAPG

0.21

12.70

53.11

257.62

similar to zinc finger homeodomain 4

ZFHX4

0.23

160.03

55.13

241.22

neurotrophic tyrosine kinase, receptor, type 2

NTRK2

0.62

248.28

106.60

172.40

synaptosomal-associated protein, 25 kDa

SNAP25

0.55

0.81

94.22

171.81

lectin, galactoside-binding, soluble, 1 (galectin 1)

LGALS1

0.57

81.20

88.20

155.33

testis derived transcript (3 Lin11, Isl-1 & Mec-3 (LIM) domains)

TES

0.38

32.63

55.66

145.10

Related-rat sarcoma viral (r-ras) oncogene homolog

RRAS

0.74

0.39

93.40

125.71

sorting nexin family member 30

SNX30

0.74

31.31

89.00

120.18

vanin 1

VNN1

0.69

67.28

82.51

119.73

collagen, type XVIII, alpha 1

COL18A1

1.02

102.46

116.62

114.48

transmembrane protein 100

TMEM100

1.05

1.80

116.48

110.68

macrophage migration inhibitory factor

MIF

3.47

1.70

368.05

105.96

ectodermal-neural cortex

ENC1

0.74

53.63

75.21

101.74

pleiotrophin

PTN

208.08

54.11

1.10

-189.18

cytokine-like 1

CYTL1

11388.79

19.33

29.48

-386.29

retinoic acid receptor responder 1

RARRES1

974.75

156.02

1.98

-491.73

phenylalanine hydroxylase

PAH

195.83

0.24

0.32

-612.20

integrin-binding sialoprotein

IBSP

300.90

0.06

0.37

-817.30

fibulin 1

FBLN1

199.29

0.22

0.13

-1511.93

collagen, type X, alpha 1

COL10A1

1192.84

7.19

0.79

-1518.56

peptidase inhibitor 15

PI15

478.32

83.74

0.10

-5002.83


IVD specific marker genes. Genes identified by NP vs AC microarray comparison. Mean fluorescence intensity is shown for each cell type (AC, AF and NP) along with calculated fold change values (positive and negative) between NP and AC cells that were greater than 100. Highlighted in bold are genes that were taken forward for qRT-PCR and italicised are genes that were identified in previous array studies [23,24]. AC, articular cartilage; AF, annulus fibrosus; NP, nucleus pulposus; qRT-PCR, quantitative real time polymerase chain reaction.

Minogue et al. Arthritis Research & Therapy 2010 12:R22   doi:10.1186/ar2929

Open Data