Table 1

Extracellular space genes regulated at least 1.45-fold by TNFαa

Gene

Accession number

Description

Fold change

Basal MEK/ERK dependent


U0126

TNF

TNF + U0126


TNFα-regulated MEK/ERK dependent

Hyaluronic acid binding activity

Agc1

[GenBank:NM_022190]

Aggrecan 1

1.14

0.68

1.08

Hapln1

[GenBank:NM_019189]

Hyaluronan and proteoglycan link protein 1

1.15

0.65

0.96

Collagenase or metallopeptidase activity

Mmp-12

[GenBank:NM_053963]

Matrix metallopeptidase 12

0.67

2.92

0.93

Mmp-9

[GenBank:NM_031055]

Matrix metallopeptidase 9

0.87

1.89

1.01

Metallopeptidase activity

Arts1, ERAP1, Appils

[GenBank:NM_030836]

Type 1 TNF receptor shedding aminopeptidase regulator

1.33

1.78

1.55

Complement binding

C4bpa

[GenBank:NM_012516]

Complement component 4 binding protein, alpha

1.01

2.19

1.35

Others

Amigo2

[GenBank:NM_182816]

Adhesion molecule with Ig-like domain 2

0.99

1.55

1.26

Cacna2d3

[GenBank:NM_175595]

Calcium channel, voltage-dependent, α23 subunit

0.82

1.56

0.99

Cd68 (predicted)

[GenBank:NM_001031638]

CD68 antigen

1.01

1.80

1.14

Cgref1, Cgr11

[GenBank:NM_139087]

Cell growth regulator with EF hand domain 1

1.01

0.61

0.83

Cyp4b1

[GenBank:NM_016999]

Cytochrome P450, family 4, subfamily b, polypeptide 1

1.71

1.72

1.83

Gm1960, Cinc2, Cinc-2

[GenBank:NM_138522]

Gene model 1960 (NCBI)

0.94

2.38

1.27

TNFα-regulated MEK/ERK independent

Peptidase activity

Adam17; TACE

[GenBank:NM_020306]

A disintegrin and metalloproteinase domain 17 (TNF, alpha, converting enzyme)

0.93

1.64

1.41

Mmp13

[GenBank:XM_343345]

Matrix metallopeptidase 13

0.33

6.80

1.10

*

Ctsc

[GenBank:NM_017097]

Cathepsin C

1.18

2.84

1.72

Serpinb2, Pai2a

[GenBank:NM_021696]

Serine (or cysteine) proteinase inhibitor, clade B, member 2

0.75

3.47

1.68

Plat, tPA, PATISS

[GenBank:NM_013151]

Plasminogen activator, tissue

0.94

3.22

1.56

Plau, UPAM

[GenBank:NM_013085]

Plasminogen activator, urokinase

1.36

2.23

2.87

C1s, r-gsp

[GenBank:NM_138900], [GenBank:XM_575664]

Complement component 1, s subcomponent

1.05

1.98

1.88

Cpxm1 (predicted)

[GenBank:XM_215840]

Carboxypeptidase × 1 (M14 family) (predicted)

1.21

3.11

1.84

Mmp3

[GenBank:NM_133523]

Matrix metallopeptidase 3

0.36

10.26

3.41

*

Chemokine activity

Ccl5, Scya5, Rantes

[GenBank:NM_031116]

Chemokine (C-C motif) ligand 5

0.90

4.26

1.37

Cxcl12, Sdf1

[GenBank:NM_001033882], [GenBank:NM_001033883], [GenBank:NM_022177]

Chemokine (C-X-C motif) ligand 12

0.75

2.17

1.33

Ccl20, ST38, Scya20

[GenBank:NM_019233]

Chemokine (C-C motif) ligand 20

0.65

12.86

5.82

Cx3cl1, Cx3c, Scyd1

[GenBank:NM_134455]

Chemokine (C-X3-C motif) ligand 1

0.72

4.41

2.95

Cxcl1, Gro1, CINC-1

[GenBank:NM_030845]

Chemokine (C-X-C motif) ligand 1

0.55

9.18

3.61

*

Cxcl10, IP-10, Scyb10

[GenBank:NM_139089]

Chemokine (C-X-C motif) ligand 10

0.88

2.40

3.22

Ccl2, MCP-1, Scya2, Sigje

[GenBank:NM_031530]

Chemokine (C-C motif) ligand 2

0.68

32.14

22.59

Cytokine or growth factor activity

Bmp2

[GenBank:NM_017178]

Bone morphogenetic protein 2

0.89

1.61

1.53

Gdf10

[GenBank:NM_024375]

Growth differentiation factor 10

0.59

0.30

0.21

*

Csf1

[GenBank:NM_023981]

Macrophage colony-stimulating factor 1

0.86

2.37

2.17

Ifngr1

[GenBank:NM_053783]

IFNγ receptor 1

0.96

1.97

1.39

Spp1, OSP

[GenBank:NM_012881]

Secreted phosphoprotein 1

0.97

4.21

1.98

Vegfa

[GenBank:NM_031836]

Vascular endothelial growth factor A

1.11

1.80

1.43

ATPase activity

Tap1, Cim, Abcb2

[GenBank:NM_032055]

Transporter 1, ATP-binding cassette, subfamily B (MDR/TAP)

1.22

1.91

2.24

Tap2, Cim, Abcb3

[GenBank:NM_032056]

Transporter 2, ATP-binding cassette, subfamily B (MDR/TAP)

1.01

2.11

1.91

G-protein coupled receptor binding

Ramp1

[GenBank:NM_031645]

Receptor (calcitonin) activity modifying protein 1

2.16

0.53

0.93

Ramp2

[GenBank:NM_031646]

Receptor (calcitonin) activity modifying protein 2

0.88

1.57

1.31


aGenes separated into molecular function subcategories represented in the list of gene changing at least 1.45-fold by TNFα as either mitogen-activated kinase kinase (MEK)/extracellular regulated kinase (ERK) dependent or MEK/ERK independent. Specifically defined subcategories were identified in the molecular function gene ontology as significantly represented (P < 0.01) within the MEK/ERK dependent or MEK/ERK independent lists.

Rockel et al. Arthritis Research & Therapy 2009 11:R8   doi:10.1186/ar2595

Open Data