Table 1.
Genes differentially expressed in CD4 T-cells from 2 week-old NOD mice.
| Probe set ID | Gene symbol | Fold change | Adjusted p-value | Chromosome (Chr) | T1D susceptibility region |
|---|---|---|---|---|---|
| Immune response | |||||
| 1418642_at (L) | Lcp2 | –9.65 | 0.00048 | Chr11 | - |
| 1457088_at (H) | Pldn | 5.48 | 0.00128 | Chr2 | Idd13 |
| Apoptosis/cell proliferation | |||||
| 1440493_at (L) | Galnt10 | –37.09 | 0.000217 | Chr11 | - |
| 1457812_at (L) | Trp53bp1 | –30.33 | 0.000291 | Chr2 | Idd13 |
| 1438462_x_at (L) | Khdrbs1 | –7.42 | 0.000662 | Chr4 | Idd9/11 |
| 1417714_x_at (H) | Hba-a1 | 5.36 | 0.0031 | Chr11 | - |
| 1449716_s_at (H) | Nrd1 | 2.77 | 0.00321 | Chr4 | - |
| 1439650_at (L) | Rtn4 | –5.74 | 0.00296 | Chr11 | - |
| 1440358_at (H) | Arhgef15 | 4.82 | 0.00184 | Chr11 | - |
| 1428361_x_at (L) | Hba-a1 | –4.11 | 0.00104 | Chr11 | - |
| 1444890_at (L) | Mprip | –4.08 | 0.00368 | Chr11 | - |
| 1449052_a_at (L) | Dnmt3b | –3.24 | 0.00048 | Chr2 | Idd13 |
| 1433681_x_at (L) | Capn3 | –2.30 | 0.00214 | Chr2 | Idd13 |
| Transcription | |||||
| 1458094_at (L) | Zfp407 | –6.66 | 0.00224 | Chr18 | Idd21.1 |
| 1458274_at (H) | Zfp69 | 3.06 | 0.00288 | Chr4 | - |
| 1446147_at (H) | Rbm39 | 4.15 | 0.00129 | Chr2 | Idd13 |
| Transport | |||||
| 1455735_at (H) | Ap1s3 | 4.28 | 0.000512 | Chr1 | Idd5.4a/5.4 |
| 1417963_at (H) | Pltp | 3.00 | 0.00419 | Chr2 | - |
| 1420897_at (L) | Snap23 | –1.81 | 0.000668 | Chr2 | Idd13 |
| Zinc-ion binding | |||||
| 1437432_a_at (L) | Trim12a | –769.41 | 2.45E-08 | Chr7 | Idd27 |
| 1443858_at (L) | Trim/12c (Trim5) | –238.91 | 3.05E-07 | Chr7 | Idd27 |
| Protein/nucleic acid binding | |||||
| 1424454_at (H) | Tmem87a | 13.40 | 0.00114 | Chr2 | Idd13 |
| 1455863_at (L) | Spata5l1 | –5.40 | 0.00217 | Chr2 | - |
| 1419276_at (H) | Enpp1 | 2.07 | 0.00105 | Chr10 | - |
| 1453065_at (H) | Aldh5a1 | 1.78 | 0.00337 | Chr13 | - |
| Other enzymes | |||||
| 1442424_at (L) | Ctdspl2 | –46.26 | 0.000831 | Chr2 | Idd13 |
| 1418035_a_at (L) | Prim2 | –11.25 | 5.55E-05 | Chr1 | Idd26 |
| 1423569_at (L) | Gatm | –7.41 | 0.000112 | Chr2 | Idd13 |
| 1453009_at (L) | Cpm | –6.18 | 0.00158 | Chr10 | - |
| 1416494_at (L) | Ndufs5 | –5.21 | 0.000538 | Chr4 | - |
| 1427943_at (H) | Acyp2 | 2.75 | 4.07E-05 | Chr11 | - |
| 1427302_at (H) | Enpp3 | 2.66 | 0.0027 | Chr10 | - |
| 1417826_at (L) | Akr1e1 | –6.52 | 0.000273 | Chr13 | - |
| 1455219_at (L) | Slx1b | –5.00 | 0.00184 | Chr7 | Not Assigned |
| 1442466_a_at (L) | Ppip5k1 | –4.14 | 0.00211 | Chr2 | Idd13 |
| 1444377_at (L) | Psmb2 | –3.41 | 0.0028 | Chr4 | Idd11 |
| 1435129_at (H) | Ptp4a2 | 2.37 | 0.00487 | Chr4 | Idd9/11 |
| 1454772_at (L) | Snrnp200 | –2.32 | 0.00189 | Chr2 | Idd13 |
| 1415878_at (L) | Rrm1 | –1.90 | 0.00407 | Chr7 | - |
| 1451998_at (L) | Tasp1 | –1.78 | 0.000499 | Chr2 | Idd13 |
| Other (unknown transcripts are indicated below in the legend) | |||||
| 1444741_at (L) | Dock2 | –144.49 | 3.18E-06 | Chr11 | - |
| 1436061_at (L) | Chaf1a | –21.85 | 0.000538 | Chr17 | - |
| 1442824_at (L) | Raly | –13.69 | 0.000313 | Chr2 | Idd13 |
| 1452426_x_at (L) | LOC433762 | –12.00 | 0.000549 | Chr4 | - |
| 1452359_at (L) | Rell1 | –2.53 | 0.000662 | Chr5 | - |
| 1457822_at (L) | Tmem131 | –13.55 | 0.00438 | Chr1 | Idd26 |
| 1445214_at (L) | Rex2 | –9.26 | 0.000783 | Chr4 | Idd9.2 |
| 1456635_at (L) | Sp110 | –8.01 | 0.00156 | Chr1 | Idd5.4a/5.4 |
| 1428587_at (L) | Tmem41b | –4.36 | 0.000289 | Chr7 | Idd27 |
| 1424509_at (H) | Cd177 | 4.03 | 0.00284 | Chr7 | - |
| 1435792_at (H) | Csprs | 3.86 | 0.00199 | Chr1 | Idd5.4a/5.4 |
| 1458684_at (H) | Ss18 | 2.77 | 0.00407 | Chr18 | Idd21.3 |
| 1424721_at (L) | Mfap3 | –2.54 | 0.000895 | Chr11 | - |
| 1425331_at (L) | Zfp106 | –2.10 | 0.00183 | Chr2 | Idd13 |
Statistical analysis (1-way-ANOVA; p < 0.005, Benjamini–Hochberg) followed by hierarchical clustering identified 58 differentially expressed probe sets (representing 56 different genes) at 2 weeks; L and H, respectively, indicate lower or higher expression in NOD mice compared to control mice, NOR and C57BL/6. Two unknown transcripts (both on Chr4) included: 9930104L06Rik (L) and 2510039O18Rik (L; Idd9.2). Fold change (FC) was calculated by ratio of means of expression in NOD mice versus controls. Dashes indicate those genes are not located within a known T1D susceptibility region (Idd); all indicated Idds (except one, Idd5.4a/5.4) were identified as conferring resistance to diabetes (http://www.t1dbase.org). Genes highlighted in bold font were differentially expressed at all 3 ages, 2, 3 and 4 weeks.