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Table 2 Differentially expressed genes in patients with polyarticular rheumatoid polyarthritis (n = 9) and healthy controls (n = 12)

From: Novel approaches to gene expression analysis of active polyarticular juvenile rheumatoid arthritis

A. Genes overexpressed in acute untreated patients
Gene bank Name Description AverAD AverHC AD/HC Summary of function
S54761 B2M β2-mu, β2-microglobulin 266.2 57.5 4.6 β2-microglobulin; major component of the hemodialysis-associated amyloid fibrils
L20941 FTHL6 Ferritin heavy chain 264.8 90.3 2.9 Ferritin heavy polypeptide 1; iron-storage protein
M17733 TMSB4X Thymosin β4 251.7 56.1 4.5 Thymosin β4; sequesters actin monomers and inhibits actin polymerization
M11147 FTL Ferritin L chain 230.3 82.9 2.8 Ferritin light polypeptide; iron storage protein
   Homologous to elongation factor 1α 1 (PTI-1) 224.7 59.1 3.8 Homologous with a truncated and mutated form of human elongation factor 1α subunit
X04098 ACTG Cytoskeletal γ-actin 219.4 49.4 4.4 γ-actin; member of the non-muscle family of actins
X52008 GLR α2 subunit of inhibitory glycine receptor 215.9 74.5 2.9 α2 subunit of the glycine receptor chloride channel; binds strychnine and is important for inhibitory neurotransmission
M11354   H3.3 histone, class B 213.1 62.5 3.4 Member of the H3 histone family; involved in compaction of DNA into nucleosomes
Y14040 CASH CASH β protein 206.9 71.2 2.9 Caspase-like apoptosis regulatory protein; lacks caspase catalytic activity
Y13829 EXP40 MBNL protein 184.1 79.4 2.3 Strongly similar to uncharacterized KIAA0428
   CD74 158.4 67.0 2.4 HLA-DR antigens associated invariant chain
   Coactiosin-like protein 131.6 62.0 2.1 Interacts with 5-lipoxygenase
AF010187 FIBP FGF-1 intracellular binding protein (FIBP) 127.6 43.4 2.9 Acidic fibroblast growth factor intracellular binding protein; may mediate the mitogenic properties associated with acidic FGF1
M60627 FMLP N-formylpeptide receptor (fMLP-R26) 122.7 64.7 1.9 Formyl peptide receptor 1, a G protein-coupled receptor; binds bacterial N-formyl-methionyl peptides
X91257 SERRS Seryl-tRNA synthetase 111.8 59.2 1.9 Cytosolic seryl-tRNA synthetase; class II aminoacyl tRNA synthetase, aminoacylates its cognate tRNAs with serine during protein biosynthesis
L13463 G0S8 Helix-loop-helix basic phosphoprotein (G0S8) 108.9 65.2 1.7 Regulator of G-protein signalling 2; negatively regulates G protein-coupled receptor signalling; has a basic helix-loop-helix motif
M77693 SSAT Spermidine/spermine N1-acetyltransferase 108.0 34.2 3.2 Spermidine/spermine N1-acetyltransferase; catalyzes rate-limiting step in polyamine catabolism
J03077 SAP1 Co-β-glucosidase (proactivator) 107.3 37.0 2.9 Prosaposin; precursor of saposins A-D, may bind and transport gangliosides, cleavage products activate lysosomal hydrolysis of sphingolipids
X16478   5' fragment for vimentin N-terminal fragment 101.0 42.7 2.4 Intermediate filament subunit
J00068 NEM2 Adult skeletal muscle α-actin mRNA 91.7 39.8 2.3 α1 actin; skeletal muscle-specific actin
M63603 PLB Phospholamban 89.4 46.3 1.9 Phospholamban; regulates the sarcoplasmic reticulum calcium pump
K00558 K-ALPHA-1 α-tubulin 77.9 36.9 2.1 α-tubulin (k-α-1); may be part of a heterodimer that polymerizes to form microtubules; member of a family of microtubule structural proteins
D76444 KF1 hkf-1 68.0 36.0 1.9 May be associated with membranous protein sorting; contains a zinc finger domain
M27110 PLP Proteolipid protein mRNA (PLP) 51.2 28.1 1.8 Proteolipid protein; predominant protein in myelin
AF001434 HPAST Hpast (HPAST) 16.1 3.2 5.1 Very strongly similar to murine Ehd; may be involved in ligand-initiated endocytosis
M33882 IFI-78K p78 protein 11.3 1.4 8.0 Similar to murine Mx; may be a guanine nucleotide-binding protein
AB006190 AQPap mRNA for aquaporin adipose 8.4 1.8 4.8 Aquaporin 7; water and glycerol channel expressed predominantly in adipose tissue
D49489 P5 Protein disulfide isomerase-related protein P5 7.4 3.2 2.3 Member of the protein disulfide isomerase superfamily; contains two thioredoxin-like domains
X06990 BB2 Intercellular adhesion molecule-1 ICAM-1 5.8 1.5 3.8 Surface glycoprotein; binds the integrin LFA-1 (ITGB2) and promotes adhesion; member of the immunoglobulin superfamily
U39317 UBE2D2 E2 ubiquitin conjugating enzyme UbcH5B 5.7 2.4 2.4 Member of the ubiquitin-conjugating enzyme E2 subfamily; may catalyze ubiquitination of cellular proteins prior to degradation
L16842 UQCRC1 Ubiquinol cytochrome-c reductase core I protein 5.5 2.7 2.1 Core I protein; subunit of the ubiquinol-cytochrome-c oxidoreductase in the mitochondrial respiratory chain
U45448 P2X1 P2x1 receptor 4.7 1.7 2.8 Purinergic receptor 1; ligand-gated ion channel that may be gated by extracellular adenosine 5'-triphosphate (ATP)
AF083255 RHELP RNA helicase-related protein 4.3 2.2 2.0 Moderately similar to human P72; may be an ATP-dependent helicase; member of DEAD/H box family, has conserved C-terminal helicase domain
U68536 ZNF24 Zinc finger protein 4.0 1.4 2.8 Zinc finger protein 24; contains zinc fingers
B. Genes overexpressed in healthy controls
Gene bank Name Description AverAD AverHC HC/AD Summary of function
U00968 SREBP1 SREBP-1 36.0 85.2 2.4 Transcription factor; activates genes involved in lipid metabolism, translocates to the nucleus and activates transcription of the LDL receptor and H MG CoA synthase genes in sterol-depleted cells
M36072 SURF-3 Ribosomal protein L7a (surf 3) large subunit 43.5 78.2 1.8 Ribosomal protein L7a; component of the 60-S ribosomal subunit
X80909 NACA α NAC mRNA 32.9 68.0 2.1 Nascent-polypeptide-associated complex α subunit; binds nascent polypeptides and promotes the interaction between signal recognition particle and signal peptide
M15661 RPL36A Ribosomal protein L36a 35.2 59.6 1.7 Ribosomal protein L36a; component of the large 60-S ribosomal subunit
U10248 HUMRPL29 Ribosomal protein L29 (humrpl29) 27.9 48.4 1.7 Ribosomal protein L29; component of the large 60-S ribosomal subunit, also functions as a cell surface heparin/heparan sulfate (HP/HS)-binding protein
M33294 TNF-R Tumor necrosis factor receptor 10.6 32.4 3.1 Type I tumor necrosis factor receptor; mediates proinflammatory cellular responses; contains a juxtamembrane domain
D15050 AREB6 Transcription factor AREB6 14.6 32.4 2.2 Transcriptional modulator; inhibits interleukin-2 expression in T lymphocytes; contains a zinc finger domain
U54559 EIF3S3 Translation initiation factor eIF3 p40 subunit 12.6 30.5 2.4 Translation initiation factor 3, subunit 3 (γ, 40 kDa); subunit of the complex that stabilizes initiator Met-tRNA binding to 40-S subunits
U46751 P60 Phosphotyrosine independent ligand p62 9.5 29.1 3.1 Ubiquitin-binding protein; binds SH2 domain of p56lck and ubiquitin; contains G-protein-binding region, PEST and cys-rich zinc-finger-like motifs
AF017305 Unph Deubiquitinating enzyme UnpEL (UNP) 11.4 21.7 1.9 Strongly similar to murine Unp; removes ubiquitin from ubiquitin-conjugated proteins; member of the ubiquitin-specific cysteine (thiol) protease family
M57567 ARF5 ADP-ribosylation factor (hARF5) 6.5 15.4 2.4 ADP-ribosylation factor 5, a GTP-binding protein; stimulates cholera toxin activity, may be involved in vesicular intracellular transport
U02609 TBL3 Transducin-like protein 5.3 9.3 1.8 Contains WD40 repeats
   NEDD5 3.0 9.0 3.0 Role of Nedd5 in neurite outgrowth
   CAPON 4.1 8.1 2.0 C-terminal PDZ domain ligand of neuronal nitric oxide synthase.
   Adenylate cyclase, type VII 3.4 6.4 1.9 Adenylate cyclase (type 7), an ATP-pyrophosphate lyase; converts ATP to cAMP
C. Genes expressed in active untreated patients only
Gene bank Name Description AverAD AverHC   Summary of function
D14874 PROAM-N20 Adrenomedullin 6.8 ND   Precursor of adrenomedullin (AM) and the putative 20-amino-acid peptide proAM-N20; regulates blood pressure and heart rate
X86556 ACADVL HVLCAD gene 2.8 ND   Very-long-chain-acyl-coenzyme-A dehydrogenase; oxidizes straight-chain acyl-CoAs
X78873 PPP1R2 Inhibitor 2 gene 2.6 ND   Inhibitory subunit 2 of protein phosphatase 1; associates with the γ isoform of protein phosphatase 1
M28099 FBP Folate-binding protein (FBP) 1.4 ND   Adult folate-binding protein 1 (folate receptor α); binds and initiates transport of folate and methotrexate
U60800 CD100 Semaphorin (CD100) 1.4 ND   Member of the semaphorin family of chemorepellant proteins; induces B lymphocytes to aggregate and promotes their differentiation
M83233 HTF4A Transcription factor (HTF4A) 1.2 ND   Transcriptional activator; binds to the immunoglobulin enhancer E-box consensus sequence; contains a basic helix-loop-helix domain
M22430 PLA2L RASF-A PLA2 0.9 ND   Group IIA secretory phospholipase A2; hydrolyzes the phospholipid sn-2 ester bond, releasing a lysophospholipid and a free fatty acid; similar to murine Pla2g2a
AF005080 XP5 Skin-specific protein (xp5) 0.9 ND   Skin-specific protein
U96759 VBP-1 von-Hippel–Lindau-binding protein (VBP-1) 0.8 ND   von-Hippel–Lindau-binding protein; binds tumor suppressor VHL and forms a complex with VHL protein; has a consensus site for tyrosine phosphorylation
X59498 TBPA Ttr mRNA for transthyretin 0.7 ND   Transthyretin (prealbumin); carrier protein, transports thyroid hormones and retinol in the plasma
L25665 HSR1 GTP-binding protein (HSR1) 0.6 ND   Putative GTP-binding protein
U24163 FZRB Frizzled related protein Frzb precursor (fzrb) 0.6 ND   Frizzled-related protein; similar to frizzled family of receptors
X78031 FUCT-VII α-1,3-fucosyl-transferase 0.4 ND   Leukocyte α-1,3-fucosyltransferase; functions in selectin ligand synthesis
L11924 MST1 Macrophage-stimulating protein (MST1) 0.4 ND   Proapoptotic when overexpressed; binds p53
M26393   Short-chain-acyl-CoA dehydrogenase 0.4 ND   Short-chain-acyl-coenzyme-A dehydrogenase; may act in the first step in beta-oxidation of C4–C6 fatty acids; strongly similar to murine Acads
U25033 NNAT Neuronatin α 0.4 ND   Neuronatin; possibly functions to regulate ion channels during brain development
X95073 TRAX Translin-associated protein X 0.4 ND   Interacts with translin (TSN)
U63336 CAT56 MHC class I region proline-rich protein 0.4 ND   Undefined
D. Genes expressed in healthy controls only
Gene bank Name Description AverAD AverHC   Summary of function
X57637 GGTA mRNA involved in tapetochoroidal dystrophy ND 1.3   Component A of geranylgeranyl transferase; modifies Rab proteins; has similarity to guanine nucleotide dissociation inhibitors
Z11566 PR22 Pr22 protein ND 0.5   Stathmin (oncoprotein 18), a cytosolic phosphoprotein
  1. AverAD, AverHC, average expression level (defined as the number of standard deviations from mean of background) in untreated patients with active disease and in healthy controls, respectively. ND, none detected