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Table 3 Deregulated genes in the arthritic synovial fibroblast as revealed by DNA microarrays

From: Functional analysis of an arthritogenic synovial fibroblast

Fold change    
A B P a 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
  1. 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. 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.