Table 3.
Microarray Data: Transcripts Most Significantly Regulated across All Patients and Controls
| Probe set ID | Gene title | Raw expression values |
Fold change |
|||||
|---|---|---|---|---|---|---|---|---|
| AIBM | NIBM | HCTRL | q value (%) | AIBM/HCTRL | AIBM/NIBM | NIBM/HCTRL | ||
| 205132_at | Actin, α, cardiac muscle 1 | 9926.55 | 5275.13 | 338.44 | 0.00 | 29.33 | 1.88 | 15.59 |
| 201891_s_at⁎ | β-2-Microglobulin | 12,436.09 | 11,093.17 | 1570.33 | 0.00 | 7.92 | 1.12 | 7.06 |
| 216526_x_at⁎ | MHC, class I, B; MHC, class I, C; MHC class I polypeptide-related sequence A; MHC class I polypeptide-related sequence B | 8959.71 | 7976.71 | 705.27 | 0.00 | 12.70 | 1.12 | 11.31 |
| 209140_x_at⁎ | MHC, class I, B; MHC, class I, C; MHC class I polypeptide-related sequence A; MHC class I polypeptide-related sequence B | 9521.62 | 7469.66 | 297.92 | 0.00 | 31.96 | 1.27 | 25.07 |
| 217456_x_at⁎ | MHC, class I, E | 1503.90 | 827.43 | 75.69 | 0.00 | 19.87 | 1.82 | 10.93 |
| 200905_x_at⁎ | MHC, class I, E | 3383.98 | 1638.89 | 57.90 | 0.00 | 58.44 | 2.06 | 28.30 |
| 221875_x_at⁎ | MHC, class I, F | 1959.54 | 1293.23 | 101.36 | 0.00 | 19.33 | 1.52 | 12.76 |
| 211529_x_at⁎ | MHC, class I, G | 250.88 | 163.19 | 12.87 | 0.00 | 19.49 | 1.54 | 12.68 |
| 209040_s_at⁎ | Proteasome (prosome, macropain) subunit, β type, 8 (large multifunctional peptidase 7) | 1751.19 | 613.20 | 4.05 | 0.00 | 432.37 | 2.86 | 151.40 |
| 202296_s_at | RER1 retention in endoplasmic reticulum 1 homolog (Saccharomyces cerevisiae) | 16.24 | 23.27 | 706.64 | 0.00 | 0.02 | 0.70 | 0.03 |
| 200887_s_at⁎ | STAT 1, 91 kDa | 7963.49 | 6296.56 | 94.89 | 0.00 | 83.92 | 1.26 | 66.35 |
| AFFX-HUMISGF3A/M97935_3_at⁎ | STAT 1, 91 kDa | 1928.89 | 1828.85 | 34.57 | 0.00 | 55.80 | 1.05 | 52.91 |
| 221087_s_at | Apolipoprotein L, 3 | 605.96 | 373.82 | 25.70 | 5.12 | 23.58 | 1.62 | 14.55 |
| 208812_x_at⁎ | MHC, class I, C | 9337.37 | 6540.77 | 430.46 | 5.12 | 21.69 | 1.43 | 15.19 |
| 214459_x_at⁎ | MHC, class I, C | 6556.01 | 4679.25 | 371.30 | 5.12 | 17.66 | 1.40 | 12.60 |
| 204806_x_at⁎ | MHC, class I, F | 753.67 | 512.69 | 59.87 | 5.12 | 12.59 | 1.47 | 8.56 |
| 211071_s_at | Myeloid/lymphoid or mixed-lineage leukemia (trithorax homologue, Drosophila), translocated to 11 | 4511.40 | 2944.13 | 205.20 | 5.12 | 21.99 | 1.53 | 14.35 |
| 202237_at | Nicotinamide N-methyltransferase | 1944.88 | 1365.55 | 21.27 | 5.12 | 91.44 | 1.42 | 64.20 |
| 212845_at | Sterile α motif domain containing 4A | 22.95 | 44.53 | 554.77 | 5.12 | 0.04 | 0.52 | 0.08 |
| 215076_s_at | Collagen, type III, α 1 (Ehlers-Danlos syndrome type IV, autosomal dominant) | 6542.53 | 3846.48 | 12.69 | 8.84 | 515.45 | 1.70 | 303.05 |
| 213932_x_at⁎ | MHC, class I, A | 9857.13 | 7352.34 | 2127.78 | 8.84 | 4.63 | 1.34 | 3.46 |
| 201137_s_at⁎ | MHC, class II, DP β 1 | 1817.92 | 684.36 | 37.08 | 8.84 | 49.02 | 2.66 | 18.46 |
| 225061_at | DnaJ (Hsp40) homologue, subfamily A, member 4 | 1906.51 | 1525.02 | 29.68 | 11.67 | 64.24 | 1.25 | 51.39 |
| 211528_x_at⁎ | MHC, class I, G | 195.97 | 149.47 | 16.23 | 11.67 | 12.08 | 1.31 | 9.21 |
| 200814_at⁎ | Proteasome (prosome, macropain) activator subunit 1 (PA28 α) | 4007.01 | 3496.38 | 405.11 | 11.67 | 9.89 | 1.15 | 8.63 |
| 232500_at | Chromosome 20 open reading frame 74 | 1047.84 | 210.09 | 12.61 | 14.41 | 83.07 | 4.99 | 16.66 |
| 217436_x_at⁎ | MHC, class I, J (pseudogene) | 141.93 | 114.16 | 19.59 | 14.41 | 7.24 | 1.24 | 5.83 |
| 226470_at | γ-Glutamyltransferase 7 | 51.17 | 51.41 | 1893.54 | 16.21 | 0.03 | 1.00 | 0.03 |
| 228098_s_at | Myosin regulatory light chain interacting protein | 794.08 | 85.92 | 27.30 | 16.21 | 29.09 | 9.24 | 3.15 |
| 200743_s_at | Tripeptidyl peptidase I | 1741.52 | 1749.31 | 337.65 | 16.21 | 5.16 | 1.00 | 5.18 |
| 238431_at | Transcribed locus | 1251.44 | 347.59 | 22.14 | 20.02 | 56.52 | 3.60 | 15.70 |
| 215313_x_at⁎ | MHC, class I, A | 11,623.07 | 9764.78 | 968.10 | 20.02 | 12.01 | 1.19 | 10.09 |
| 204070_at | Retinoic acid receptor responder (tazarotene induced) 3 | 3065.52 | 1516.95 | 88.87 | 20.02 | 34.49 | 2.02 | 17.07 |
| 209118_s_at | Tubulin, α 1a | 1608.79 | 1037.65 | 48.98 | 20.02 | 32.85 | 1.55 | 21.19 |
Raw expression values are provided along with fold expression changes showing regulation of transcripts in AIBM vs HCTRL, AIBM vs NIBM, and NIBM vs HCTRL. The q value mirrors the false discovery rate. The lower the q value, the higher the significance of the results across all samples (see Materials and Methods). Herein, we show transcripts that were expressed with a q value of ≤20%.
MHC, major histocompatibility complex; RER, retention in endoplasmic reticulum.
⁎
Among these 34 transcripts, 19 can be attributed to components of the classic and nonclassic HLA-I, HLA-II, IFN-γ–inducible genes and immunoproteasome components.