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, α2/δ3 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

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