Table 3

Deregulated genes in the arthritic synovial fibroblast as revealed by DNA microarrays

Fold change


A

B

Pa

Gene ID

Accesion no.


25

20

0.099

peroxisome proliferator activated protein-gamma-2

U09138

14

20

0.119

c-erbA alpha2 for thyroid hormone receptor

X07751

17

16

0.000

clusterin

L08235

12

12

0.085

matricin

L20509

8

13

0.031

laminin B1

M15525

8

10

0.064

RNA-binding protein AUF1

U11274

11

7

0.304

ribosomal protein L41

U93862

9

8

0.065

type II DNA topoisomerase beta isoform

D38046

8

8

0.122

ZO-1

D14340

7

6

0.012

Ca2+-dependent activator protein for secretion

D86214

8

5

0.317

ryanodine receptor type 3

X83934

4

8

0.051

serine/threonine-protein kinase PRP4m (PRP4m)

U48737

5

6

0.038

multifunctional aminoacyl-tRNA synthetase

AA048927

6

5

0.017

p53-associated cellular protein PACT

U28789

5

6

0.021

alpha-adaptin (C)

X14972

5

5

0.007

splicing factor; arginine/serine-rich 7 (SFRS7)

AA408185

5

5

0.053

Y box transcription factor (MSY-1)

M62867

5

5

0.014

ASF

X66091

4

6

0.053

stromelysin PDGF responsive element binding protein transcription factor

U20282

6

4

0.127

translation initiation factor (Eif4g2)

U63323

5

4

0.153

ubiquitin-conjugating enzyme UbcM2

AF003346

5

4

0.065

DNA topoisomerase I

D10061

6

3

0.082

calcyclin

M37761

5

4

0.055

activin receptor (ActR)

M65287

5

3

0.112

putative RNA helicase and RNA dependent ATPase (mDEAH9)

AF017153

3

5

0.051

small nuclear RNA (Rnu1a-1)

L15447

-5

-3

0.014

gC1qBP gene

AJ001101

-5

-3

0.013

primase small subunit

D13544

-5

-3

0.071

T-cell specific protein s

L38444

-5

-3

0.064

complement receptor (Crry) gene

M34173

-2

-6

0.168

primary response gene B94

L24118

-5

-3

0.033

ferritin L-subunit

L39879

-2

-6

0.414

C/EBP delta

X61800

-5

-4

0.092

tropomyosin isoform 2

M22479

-6

-3

0.136

serine proteinase inhibitor (SPI3)

U25844

-7

-2

0.145

interferon beta (type 1)

V00755

-3

-6

0.019

TSC-22 mRNA

X62940

-3

-7

0.013

novel GTP-binding protein

D10715

-4

-6

0.039

core-binding factor

L03279

-8

-2

0.125

G-protein-like LRG-47

U19119

-5

-5

0.016

SIG41

X80232

-5

-5

0.017

BAP31

X81816

-6

-5

0.000

Rat translational initiation factor (eIF-2) alpha subunit

AA408104

-3

-8

0.048

latent TGF-beta binding protein-2

AF004874

-7

-4

0.011

endothelial monocyte-activating polypeptide I

U41341

-7

-4

0.007

beta proteasome subunit (Lmp3)

U65636

-7

-4

0.075

histone H2A.Z (H2A.Z)

U70494

-9

-3

0.029

NAD-dependent methylenetetrahydrofolate dehydrogenase-methenyltetrahydrofolate cyclohydrolase

J04627

-7

-5

0.059

fibrillin (Fbn-1)

L29454

-7

-5

0.031

calumenin

U81829

-8

-4

0.023

TIMP-3 gene for metalloproteinase-3 tissue inhibitor

Z30970

-7

-5

0.006

Cctb mRNA for CCT (chaperonin containing TCP-1) beta subunit

Z31553

-7

-6

0.036

Nedd5 mRNA for DIFF6- or CDC3,10,11,12-like

D49382

-8

-5

0.060

cadherin-associated protein (CAP102/alpha catenin)

D90362

-9

-4

0.338

OTS-8

M73748

-7

-6

0.183

20S proteasome subunit Lmp7 (Lmp7d allele)

U22031

-5

-8

0.202

ornithine aminotransferase

X64837

-4

-10

0.050

Chromosome segregation protein CUT3

AA241064

-7

-7

0.183

small heat-shock protein (HSP25)

L07577

-5

-9

0.009

triosephosphate isomerase

X53333

-10

-4

0.024

Sec61 protein complex gamma subunit

U11027

-9

-5

0.010

SPARC

X04017

-11

-4

0.025

Mer

D73368

-8

-7

0.002

IFN-gamma induced (Mg11)

U15635

-15

-2

0.129

lysyl oxidase

L04262

-9

-8

0.100

proteasome (lmp2)

L11613

-13

-4

0.059

DNA topoisomerase II

D12513

-9

-9

0.006

cytochrome c gene (MC1)

X01756

-12

-6

0.004

destrin

W08453

-12

-7

0.027

deleted in split hand/split foot 1 homologue (Dss1)

U41626

-13

-7

0.013

adenine nucleotide translocase-1 (Ant1)

U27315

-18

-2

0.215

major excreted protein (MEP).

X06086

-15

-5

0.137

osteopontin

X51834

-11

-11

0.075

integral membrane phosphoprotein band

U17297

-18

-4

0.027

phosphatase 2A B' alpha3 regulatory subunit

U59418

-11

-11

0.038

p85SPR

U96634

-12

-11

0.036

ubiquitinating enzyme E2-20K

U19854

-11

-12

0.006

brain factor-1 (Hfhbf1)

U36760

-13

-11

0.072

synaptonemal complex protein Sc65

AA028785

-12

-12

0.009

mevalonate pyrophosphate decarboxylase

AA059528

-14

-11

0.061

MO15-associated kinase (MO15)

U11822

-12

-13

0.031

overexpressed and amplified in teratocarcinoma cell line ECA39

X17502

-13

-12

0.109

DNA-polymerase delta catalytic subunit.

Z21848

-12

-14

0.114

alanyl-tRNA synthetase

AA254996

-15

-11

0.035

pituitary tumor-specific transforming factor

AA711028

-19

-7

0.041

neural precursor mRNA

D85414

-15

-11

0.107

protective protein (Mo54)

J05261

-15

-11

0.044

C57BL/6 Ly-49D-GE antigen

U10090

-12

-15

0.169

histone H2A.Z

AA285607

-11

-16

0.031

bcl-2 binding protein BAG-1

U17162

-17

-11

0.005

antigen (homologue of human CD9 antigen)

C80730

-18

-10

0.002

adenine nucleotide translocase-1 (Ant1)

U27315

-18

-11

0.080

laminin

J02870

-14

-15

0.036

protective protein (Mo54)

J05261

-11

-18

0.210

keratinocyte lipid-binding protein

X70100

-14

-16

0.253

manganese superoxide dismutase (MnSOD)

X04972

-12

-18

0.155

MyD118, a myeloid differentiation primary response gene

X54149

-15

-16

0.007

glutamate dehydrogenase

X57024

-14

-18

0.505

cytosolic aspartate aminotransferase isoenzyme1

J02623

-16

-16

0.010

voltage-dependent anion channel 1 mRNA

U30840

-17

-15

0.059

fractalkine

U92565

-17

-15

0.044

alpha glucosidase II beta subunit

U92794

-15

-17

0.038

glutamate dehydrogenase.

X57024

-21

-12

0.069

p53 cellular tumor antigen

K01700

-19

-14

0.020

bcl-2 binding protein BAG-1

U17162

-22

-12

0.051

FKBP65 binding protein mRNA, complete cds

L07063

-18

-16

0.022

hepatoma transmembrane kinase ligand

L38847

-19

-16

0.022

hypothetical E. coli protein

AA271603

-23

-12

0.091

talin

X56123

-24

-12

0.086

alpha-1 type IV collagen (Col4a-1)

J04694

-19

-17

0.007

S-adenosyl homocysteine hydrolase (ahcy)

L32836

-16

-20

0.054

UBcM4 protein

X97042

-21

-16

0.098

cadherin-11

AA184551

-17

-20

0.012

YL-1 protein

D43643

-23

-14

0.199

alpha-B crystallin

M63170

-23

-14

0.155

TDAG51

U44088

-18

-19

0.088

chop-10

X67083

-21

-17

0.033

3-oxoacyl-CoA thiolasee

C79215

-23

-15

0.171

alpha-B2-crystallin

M73741

-23

-15

0.134

reduced folate carrier (RFC1)

U32469

-28

-11

0.079

Ubiquinol-cytochrome C reductase complex 6.4 KD protein

AA198790

-27

-13

0.255

epimorphin

D10475

-22

-18

0.004

alpha-2 type IV collagen

J04695

-21

-19

0.027

acrogranin

M86736

-29

-11

0.013

endogenous murine leukemia virus modified polytropic provirus DNA

M17327

-20

-20

0.023

C3H cytochrome P450 (Cyp1b1)

U03283

-21

-21

0.005

delta-aminolevulinate dehydratase

X13752

-22

-21

0.058

U1 snRNP-specific protein C

U70315

-27

-16

0.058

HN1

U90123

-28

-17

0.145

mMIS5

D86726

-37

-11

0.104

proteasome subunit MECL1.

D85561

-22

-26

0.063

growth factor-induced delayed early response protein

L02914

-21

-27

0.121

TAP2-d

U60087

-27

-23

0.007

RNA polymerase I 40 kD subunit

D31966

-16

-34

0.212

Ma

X62742

-38

-13

0.282

argininosuccinate synthetase (Ass)

M31690

-31

-22

0.087

Gas 5 growth arrest specific protein

X59728

-27

-26

0.006

mama

X67809

-26

-27

0.031

Cctz mRNA for CCT (chaperonin containing TCP-1) zeta

Z31557

-34

-20

0.185

hypothetical 28.4 KD protein

AA617493

-22

-37

0.148

H2-M alpha, H2-M beta 2, H2-M beta 1, Lmp2

U35323

-39

-35

0.056

metaxin

L36962

-41

-39

0.060

Ubiquinol-cytochrome C reductase complex 7.2 KD protein

AA237529

-49

-43

0.022

hypothetical 26.5 KD protein

AA122622


Deregulation is expressed as fold change of gene expression after global normalization, which is an estimate of the transcript abundance between the control and experimental samples, as determined by the Affymetrix software http://www.affymetrix.com webcite. Negative values indicate downregulation A and B refer to duplicate samples that differ by 10 passages. aCalculated with paired t-test for the average difference changes between the samples http://www.affymetrix.com webcite.

Aidinis et al. Arthritis Res Ther 2003 5:R140-R157   doi:10.1186/ar749

Open Data