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. 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.