Table 2.
Genes differentially expressed in CD4 T-cells from 3 week-old NOD mice (continued in Table 3).
| Probe set ID | Gene symbol | Fold change | Adjusted p-value | Chromosome (Chr) | T1D susceptibility region |
|---|---|---|---|---|---|
| Immune response | |||||
| 1418642_at (L) | Lcp2 | –12.20 | 0.00339 | Chr11 | - |
| 1457088_at (H) | Pldn | 5.67 | 0.000481 | Chr2 | Idd13 |
| 1448550_at (L) | Lbp | –3.98 | 0.000176 | Chr2 | Idd13 |
| 1435529_at (L) | Ifit1lb | –2.91 | 0.00242 | Chr19 | - |
| 1460394_a_at (H) | Inppl1 | 2.76 | 0.00318 | Chr7 | - |
| 1450783_at (L) | Ifit1 | –2.73 | 0.00395 | Chr19 | - |
| 1424775_at (L) | Oas1a | –2.20 | 0.00115 | Chr5 | - |
| 1418580_at (L) | Rtp4 | –2.10 | 0.00317 | Chr16 | - |
| 1448940_at (L) | Trim21 | –2.03 | 0.00399 | Chr7 | Idd27 |
| 1435560_at (L) | Itgal | –1.84 | 0.00242 | Chr7 | Not Assigned |
| 1452956_a_at (L) | Ifi27 | –1.74 | 0.00484 | Chr6 | |
| Apoptosis/cell proliferation | |||||
| 1457812_at (L) | Trp53bp1 | –16.30 | 0.000964 | Chr2 | Idd13 |
| 1440493_at (L) | Galnt10 | –11.41 | 0.000748 | Chr11 | - |
| 1417714_x_at (H) | Hba-a1 | 10.69 | 0.000156 | Chr11 | - |
| 1438462_x_at (L) | Khdrbs1 | –5.59 | 0.000211 | Chr4 | Idd9/11 |
| 1449716_s_at (H) | Nrd1 | 2.36 | 0.00133 | Chr4 | - |
| 1452677_at (H) | Pnpt1 | 13.80 | 0.0012 | Chr11 | - |
| 1440319_at (L) | Mef2a | –13.53 | 0.00227 | Chr7 | - |
| 1444890_at (L) | Mprip | –9.37 | 0.00439 | Chr11 | - |
| 1439650_at (L) | Rtn4 | –5.24 | 0.00318 | Chr11 | - |
| 1433681_x_at (L) | Capn3 | –2.89 | 0.000442 | Chr2 | Idd13 |
| 1428819_at (L) | Mapre1 | –2.78 | 0.00242 | Chr2 | Idd13 |
| 1449052_a_at (L) | Dnmt3b | –2.77 | 1.06E-05 | Chr2 | Idd13 |
| 1436647_at (H) | Ttbk2 | 2.69 | 0.00254 | Chr2 | Idd13 |
| 1419269_at (H) | Dut | 2.54 | 0.0016 | Chr2 | Idd13 |
| 1444500_at (L) | Ahsa1 | –2.48 | 0.0042 | Chr12 | - |
| 1436025_at (H) | Ccdc88a | 2.40 | 0.000697 | Chr11 | - |
| 1441937_s_at (L) | Pink1 | –2.11 | 0.00159 | Chr4 | - |
| 1448184_at (L) | Fkbp1a | –1.94 | 0.00449 | Chr2 | Idd13 |
| 1422808_s_at (L) | Dock2 | –1.84 | 0.000999 | Chr11 | - |
| 1457813_at (H) | Trp53bp1 | 1.62 | 0.0044 | Chr2 | Idd13 |
| 1448027_at (L) | Ncoa3 | –1.47 | 0.00277 | Chr2 | - |
| 1419562_at (L) | Birc6 | –1.31 | 0.00393 | Chr17 | - |
| Transcription | |||||
| 1458094_at (L) | Zfp407 | –8.70 | 0.000878 | Chr18 | Idd21.1 |
| 1458274_at (H) | Zfp69 | 3.25 | 0.00264 | Chr4 | - |
| 1449592_at (H) | Tcf15 | 10.64 | 0.000988 | Chr2 | Idd13 |
| 1459026_at (L) | Snw1 | –10.00 | 0.00152 | Chr12 | |
| 1417961_a_at (L) | Trim30 | –7.39 | 2.84E-05 | Chr7 | Idd27 |
| 1445214_at (L) | Zfp715 | –4.30 | 0.000612 | Chr7 | - |
| 1447703_x_at (L) | Zfp593 | –4.09 | 5.47E-05 | Chr4 | - |
| 1442356_at (L) | Max | –2.24 | 0.00491 | Chr12 | - |
| 1426765_at (L) | Commd7 | –2.09 | 0.000466 | Chr2 | Idd13 |
| 1436416_x_at (L) | Fxc1 | –1.81 | 6.23E-05 | Chr7 | Idd27 |
| 1450350_a_at (L) | Jdp2 | –1.39 | 0.00475 | Chr12 | - |
| Transporters | |||||
| 1460617_s_at (L) | Rab6b | –15.69 | 0.000612 | Chr9 | - |
| 1458426_at (L) | Kif1b | –3.72 | 0.000704 | Chr4 | Idd9.2 |
| 1455735_at (H) | Ap1s3 | 3.09 | 0.00386 | Chr1 | Idd5.4a/5.4 |
| 1424615_at (L) | Pgap2 | –2.18 | 0.0019 | Chr7 | Idd27 |
| 1424211_at (H) | Slc25a33 | 1.83 | 0.0012 | Chr4 | - |
| Zinc-ion binding | |||||
| 1437432_a_at (L) | Trim12a | –252.63 | 1.20E-08 | Chr7 | Idd27 |
| 1443858_at (L) | Trim12c (Trim5) | –140.08 | 5.39E-07 | Chr7 | Idd27 |
| 1435665_at (L) | Trim30d | –3.16 | 0.00227 | Chr7 | Idd27 |
Statistical analysis (1-way-ANOVA; p < 0.005, Benjamini–Hochberg) followed by hierarchical clustering identified 115 differentially expressed probe sets (representing 107 different genes) at 3 weeks; L and H, respectively, indicate lower or higher expression in NOD mice compared to control mice, NOR and C57BL/6. This table shows a partial list of the genes; the remaining genes are shown in Table 3. 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.