Table 3 Genes differentially expressed in OA meniscal cells compared to normal meniscal cells.

Immune response

HLA-DPA1

M27487

5.3

Major histocompatibility complex, class II, DP alpha 1

IFI6

NM_022873

2.0

Interferon, alpha-inducible protein 6

CFH

X04697

1.7

Complement factor H

CTSS

NM_004079

1.6

Cathepsin S

FYN

S74774

1.5

FYN oncogene related to SRC, FGR, YES

ILF2

NM_004515

-1.3

Interleukin enhancer binding factor 2, 45 kDa

PSMB9

AI375915

-1.2

Proteasome (prosome, macropain) subunit, beta type, 9

Inflammatory

Response

ITGB2

NM_000211

6.6

Integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)

CFH

X04697

1.7

Complement factor H

BDKRB2

NM_000623

1.3

Bradykinin receptor B2

Cytokine production

SRGN

NM_002727

2.8

Serglycin

ARNT

AI768497

2.3

Aryl hydrocarbon receptor nuclear translocator

INHBA

M13436

1.9

Inhibin, beta A

Calcium ion transport

CACNA1C

F11066

1.5

Calcium channel, voltage-dependent, L type, alpha 1C subunit

FYN

S74774

1.5

FYN oncogene related to SRC, FGR, YES

CHRNB2

NM_000748

1.4

Cholinergic receptor, nicotinic, beta 2 (neuronal)

Biomineral formation

ENPP1

BF057080

1.7

Ectonucleotide pyrophosphatase/phosphodiesterase 1

SRGN

NM_002727

2.8

Serglycin

ACVR2A

AI149508

1.5

Activin A receptor, type IIA

Cell proliferation

ITGB2

NM_000211

6.6

Integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)

FGF7

NM_002009

4.1

Fibroblast growth factor 7 (keratinocyte growth factor)

ELN

AA479278

2.5

Elastin (supravalvular aortic stenosis, Williams-Beuren syndrome)

IGFBP7

NM_001553

2.4

Insulin-like growth factor binding protein 7

SKAP2

AB014486

2.2

Src kinase associated phosphoprotein 2

ARNT

AI768497

2.3

Aryl hydrocarbon receptor nuclear translocator

FOXO1

NM_002015

1.5

Forkhead box O1

BCAT1

AL390172

1.5

Branched chain aminotransferase 1, cytosolic

ACVR2A

AI149508

1.5

Activin A receptor, type IIA

TCF7L2

AA664011

1.4

Transcription factor 7-like 2 (T-cell specific, HMG-box)

CHRNB2

NM_000748

1.4

Cholinergic receptor, nicotinic, beta 2 (neuronal)

TCFL5

NM_006602

1.2

Transcription factor-like 5 (basic helix-loop-helix)

NRP1

AA609131

-1.3

Neuropilin 1

PHB

AL560017

-1.3

Prohibitin

TBX5

NM_000192

-1.3

T-box 5

NCK2

BC000103

-1.2

NCK adaptor protein 2

PRPF19

NM_014502

-1.2

PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae)

Integrin-mediated signaling pathway

ITGB2

NM_000211

6.6

Integrin, beta 2

ITGB8

BF513121

3.6

Integrin, beta 8

ITGA11

AF109681

1.5

integrin, alpha 11

GAB2

NM_012296

1.5

GRB2-associated binding protein 2

Skeletal system/Tissue development

DSP

NM_004415

5.2

Desmoplakin

FGF7

NM_002009

4.2

Fibroblast growth factor 7 (keratinocyte growth factor)

SRGN

NM_002727

2.8

Serglycin

INHBA

M13436

1.9

Inhibin, beta A

TIMP3

AW338933

1.7

TIMP metallopeptidase inhibitor 3

ENPP1

BF057080

1.7

Ectonucleotide pyrophosphatase/phosphodiesterase 1

COL5A1

N30339

1.7

Collagen, type V, alpha 1

ACVR2A

AI149508

1.5

Activin A receptor, type IIA

FBN1

AW955612

1.4

Fibrillin 1

BARX1

NM_021570N

-1.9

BARX homeobox 1

GABBR1

NM_001470

-1.9

Gamma-aminobutyric acid (GABA) B receptor, 1

HOXA11

H94842

-1.5

Homeobox A11

CHST11

NM_018413

-1.5

Carbohydrate (chondroitin 4) sulfotransferase 11

NSDHL

BC000245

-1.4

NAD(P) dependent steroid dehydrogenase-like

ZNRD1

AF230337

-1.3

Zinc ribbon domain containing 1

SMURF1

AF199364

-1.3

SMAD specific E3 ubiquitin protein ligase 1

DNA repair

ZSWIM7

BE645222

-1.6

Zinc finger, SWIM-type containing 7

WDR33

AB044749

-1.5

WD repeat domain 33

ASF1A

NM_014034

-1.5

ASF1 anti-silencing function 1 homolog A (S. cerevisiae)

ATM

U82828

-1.3

ataxia telangiectasia mutated

PMS2L1

AI375694

-1.3

Postmeiotic segregation increased 2-like 1

ALKBH2

AI865555

-1.2

AlkB, alkylation repair homolog 2 (E. coli)

XRCC6

NM_001469

-1.2

X-ray repair complementing defective repair in Chinese hamster cells 6

DCLRE1A

D42045

-1.2

DNA cross-link repair 1A (PSO2 homolog, S. cerevisiae)

PRPF19

NM_014502

-1.2

PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae)

ELN

AA479278

2.5

Elastin (supravalvular aortic stenosis, Williams-Beuren syndrome)

Cellular biosynthetic process

PITX2

NM_000325

-6.4

Paired-like homeodomain 2

NR3C2

NM_000901

-5.8

Nuclear receptor subfamily 3, group C, member 2

GALNT6

AW014155

-4.5

Polypeptide N-acetylgalactosaminyltransferase 6

RGMB

BE855765

-2.7

RGM domain family, member B

FOXF2

NM_001452

-2.2

Forkhead box F2

ZNF529

AL109722

-2.1

Zinc finger protein 529

BARX1

NM_021570

-1.9

BARX homeobox 1

DHODH

M94065

-1.9

Dihydroorotate dehydrogenase

LMO4

BC003600

-1.8

LIM domain only 4

BRWD1

NM_018963

-1.7

Bromodomain and WD repeat domain containing 1

TARS2

NM_025150

-1.7

Threonyl-tRNA synthetase 2, mitochondrial (putative)

HLX

M60721

-1.7

H2.0-like homeobox

BNC2

AI767962

-1.7

Basonuclin 2

PGD

NM_002631

-1.6

Phosphogluconate dehydrogenase

MEIS1

AL832770

-1.6

Meis homeobox 1

ZNF420

AI339586

-1.6

Zinc finger protein 420

ZFP28

AA831323

-1.5

Zinc finger protein 28 homolog (mouse)

CARS2

NM_024537

-1.5

Cysteinyl-tRNA synthetase 2, mitochondrial (putative)

HOXA11

H94842

-1.5

Homeobox A11

PDLIM1

BC000915

13.2

PDZ and LIM domain 1 (elfin)

ITGB2

NM_000211

6.6

Integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)

LMCD1

NM_014583

3.5

LIM and cysteine-rich domains 1

KRT7

BC002700

3.1

Keratin 7

ARNT

AI768497

2.3

Aryl hydrocarbon receptor nuclear translocator

ZNF415

NM_018355

2.2

Zinc finger protein 415

ZNF630

AK000580

2.0

Zinc finger protein 630

INHBA

M13436

1.9

Inhibin, beta A

GALNT1

U41514

1.7

Polypeptide N-acetylgalactosaminyltransferase 1

ENPP1

BF057080

1.7

Ectonucleotide pyrophosphatase/phosphodiesterase 1

Miscellaneous

PTGES

AF010316

3.2

Prostaglandin E synthase

ADAMTS5

NM_007038

1.7

ADAM metallopeptidase with thrombospondin type 1 motif, 5 (aggrecanase-2)

DSP

NM_004415

5.2

Desmoplakin

FMOD

NM_002023

2.7

Fibromodulin

sFRP4

AW089415

3.4

Secreted frizzled-related protein 4

MCAM

M28882

2.3

Melanoma cell adhesion molecule

TNXB

NM_004381

-1.3

Tenascin XB

FUS

NM_004960

-1.5

Fusion (involved in t(12;16) in malignant liposarcoma)

TBX5

NM_000192

-1.3

T-box 5