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 | Â | 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 |
| Â | Â | CD74 | 158.4 | 67.0 | 2.4 | HLA-DR antigens associated invariant chain |
| Â | Â | 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 | Â | 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 |
| Â | Â | NEDD5 | 3.0 | 9.0 | 3.0 | Role of Nedd5 in neurite outgrowth |
| Â | Â | CAPON | 4.1 | 8.1 | 2.0 | C-terminal PDZ domain ligand of neuronal nitric oxide synthase. |
| Â | Â | 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 | Â | Summary of function |
D14874 | PROAM-N20 | Adrenomedullin | 6.8 | ND | Â | 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 | Â | 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 | Â | 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 | Â | 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 | Â | 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 | Â | 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 | Â | Transthyretin (prealbumin); carrier protein, transports thyroid hormones and retinol in the plasma |
L25665 | HSR1 | GTP-binding protein (HSR1) | 0.6 | ND | Â | Putative GTP-binding protein |
U24163 | FZRB | Frizzled related protein Frzb precursor (fzrb) | 0.6 | ND | Â | 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 | Â | 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 | Â | Interacts with translin (TSN) |
U63336 | CAT56 | MHC class I region proline-rich protein | 0.4 | ND | Â | Undefined |
D. Genes expressed in healthy controls only | ||||||
Gene bank | Name | Description | AverAD | AverHC | Â | Summary of function |
X57637 | GGTA | mRNA involved in tapetochoroidal dystrophy | ND | 1.3 | Â | Component A of geranylgeranyl transferase; modifies Rab proteins; has similarity to guanine nucleotide dissociation inhibitors |
Z11566 | PR22 | Pr22 protein | ND | 0.5 | Â | Stathmin (oncoprotein 18), a cytosolic phosphoprotein |