Table 1.
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Table 1A. Gene ontology of differentially expressed transcripts identifed by microarray
| ||||
|---|---|---|---|---|
| Gene symbol | Description | Ratio anergic: naïve
|
Ontologic categories | |
| B6 | MRL | |||
| Genes increased 2-fold or more in B6 relative to MRL anergic B cells. | ||||
| Loh11cr2a | Loss of hyeterozygosity 11 | 2.85 | 0.95 | Cyc |
| Prei4 | Preimplantation protein 4 | 1.48 | 0.61 | Hydrolase, carbohydrate metabolism |
| Glipr1 | GLI pathogenesis-related 1 | 2.36 | 1.01 | Apop, Sig Trans |
| Ptpn22 | Protein tyrosine phosphatase non-receptor type 22 | 3.61 | 1.56 | Apop, Growth, Diff, Sig Trans, Dev, Phos |
| Tmbim1 | Transmembrane BAX inhibitor motif containing 1 | 2.32 | 1.05 | Alternative splicing |
| Smc2 | Structural maintenance of chrom.2 | 1.06 | 0.48 | Cyc, Nuc, chromosome organization |
| Nup153 | Nucleoporin 153 | 1.14 | 0.52 | Nuc, protein binding, transporter |
| Rb1 | Retinoblastoma 1 | 1.28 | 0.59 | Cyc, Phos, Trans reg, Diff, Prolif, Dev, Apop, Death |
| Eif4g2 | Eukaryotic translation initiation factor 4 gamma 2 | 1.10 | 0.50 | Nuc, Cyc., death, transcription initiation |
| EG622976 | 1.45 | 0.67 | none | |
| Ugdh | UDP-glucose dehydrogenase | 1.32 | 0.61 | Dev, electron transport |
| Kpna2 | karyopherin (importin) alpha 2 | 1.25 | 0.58 | DNA recombination regulation |
| Ctla4 | Cytotoxic T-lymph-assoc. protein 4 | 1.96 | 0.91 | Immune response |
| Mbnl1 | Muscleblind-like 1 | 1.85 | 0.87 | Diff, RNA binding |
| Pkib | Protein kinase inhibitor beta | 1.24 | 0.59 | Diff, kinase inhibitor |
| Birc1f | Baculoviral IAP repeat-containing 1f or Naip6 | 2.03 | 0.96 | Apop, death |
| Cept1 | choline/ethanolamine phosphor-transferase 1 | 1.52 | 0.73 | Lipid metabolism |
| Cdc2a | Cell division cycle 2 homolog A | 1.51 | 0.73 | Apop, Nuc, Cyc, Phos, mitosis, DNA damage response |
| Plekha1 | Pleckstrin homology domain containing family A | 1.22 | 0.61 | lipid binding, alternative splicing |
| Med23 | Mediator subunit SUR2 | 1.20 | 0.59 | Trans reg, metastasis suppressor |
|
Table 1B. | ||||
| Gene symbol | Description |
Ratio anergic: naïve |
Ontologic categories | |
| B6 | MRL | |||
|
Genes decreased 2-fold or more in B6 relative to MRL anergic B cells. | ||||
| Akap13 | A kinase (PRKA) anchor protein 13 or BRX | 0.91 | 1.83 | Sig Trans |
| Actc1 | Actin, alpha, cardiac | 0.93 | 1.90 | Dev, Nuc, Cytoskeletal organization |
| Tcof1 | Treacher Collins Franceschetti syndrome 1 homolog | 0.69 | 1.42 | Prolif, Phos, transport, transcription |
| Aldoart2 | Aldolase 1, A isoform, retrogene 2 | 0.91 | 1.89 | none |
| GALNAC4S-6ST | B cell Rag-Associated protein | 0.81 | 1.70 | Catalytic activity |
| Ankrd11 | Ankyrin repeat domain 11 | 1.05 | 2.20 | Nuc |
| Mef2c | Myocyte enhancer factor 2C | 0.91 | 1.92 | Apop, Diff, Phos, Trans reg, Dev |
| Grap2 | GRB2-related adaptor protein 2 | 0.65 | 1.38 | Sig Trans, cell communication |
| Ddx46 | DEAD box polypeptide 46 | 0.77 | 1.68 | Nuc, RNA binding/splicing, hydrolase |
| CD74 | CD74 antigen | 0.84 | 1.85 | Prolif, Apop, Sig Trans, Immune response |
| Phf17 | PHD finger protein 17, Jade1 | 0.81 | 1.79 | Apop, Dev, cell growth |
| Ap1gbp1 | Ap1 gamma binding protein 1 | 0.67 | 1.50 | ion binding, protein localization |
| Esco1 | Establishment of cohesion 1 | 1.16 | 2.63 | Cyc, alternative splicing, metal/ion binding |
| Igk-V1 | Ig kappa V1 | 2.06 | 4.77 | Immune Response |
| Actg2 | Actin, gamma 2, smooth muscle | 0.86 | 2.29 | Nuc, Cytoskeletal organization, Dev. |
| Mier1 | Mesoderm induct. early response-1 | 0.80 | 2.14 | Nuc, Sig Trans, Phos., Trans reg |
| Actb | Similar to cytoskeletal beta actin | 0.94 | 2.56 | Nuc, Cytoskeletal organization |
1. Genes represented by two probes are CD74 and Igk-V1. Expression ratios for one probe for each gene is shown in the table. Ratios for the second probe were 0.72 (B6) and 1.77 (MRL) for CD74, and 1.38 (B6) and 3.18 (MRL) for Igk-V1. GALNAC4S-6ST corresponds to Unigene 4631426J05Rik. Four genes or probes were omitted from the table due to absence of a known 100% homologous murine coding sequence. Operon identifiers for the omitted probes are M300017393, M300013500, M300019467, and M300013958.
2. Common GO categories: Development = Dev, Differentiation = Diff, Apoptosis = Apop, Proliferation = Prolif, Cell Cycle = Cyc, Cell Death = Death, Phosphorylation/Dephosphorylation = Phos, Transcriptional regulation = Trans reg, Signal Transduction = Sig Trans, Nucleotide binding = Nuc.
3. The ratios shown in the tables are the mean normalized values (across 4–6 chips) for the gene expression in anergic B cells relative to naive B cells for each strain. This is based on two-color competitive hybridization on each chip, pairing anergic B cell aRNA and naive B cell aRNA from the same mouse strain. The ratio of expression for each gene for each strain was generated, and these ratios were then compared between strains.