Table 1.
List of the 56 transcript genes in the TGF-β network
| Gene | Probe set | P-value | Fold change |
| ACLY | 210337_s_at | 0.051 | 1.125 |
| ASPN | 219087_at | <0.001 | 3.537 |
| BGN | 213905_x_at | <0.001 | 3.717 |
| BMP1 | 207595_s_at | 0.165 | 1.089 |
| BNIP3L | 221478_at | <0.001 | 1.406 |
| CALD1 | 212077_at | <0.001 | 1.767 |
| CAP1 | 200625_s_at | <0.001 | 2.218 |
| CAV2 | 203324_s_at | <0.001 | 1.76 |
| CFL1 | 200021_at | <0.001 | 1.695 |
| CNN3 | 201445_at | <0.001 | 2.274 |
| COL1A1 | 202310_s_at | <0.001 | 5.386 |
| COL1A2 | 202404_s_at | <0.001 | 4.89 |
| COL3A1 | 211161_s_at | <0.001 | 3.387 |
| COL4A1 | 211981_at | <0.001 | 2.469 |
| COL4A2 | 211966_at | <0.001 | 2.762 |
| COL5A1 | 212489_at | <0.001 | 2.58 |
| COL5A2 | 221729_at | <0.001 | 3.379 |
| COL6A1 | 213428_s_at | <0.001 | 2.045 |
| COL6A2 | 209156_s_at | <0.001 | 2.251 |
| COL6A3 | 201438_at | <0.001 | 2.131 |
| COLEC12 | 221019_s_at | <0.001 | 2.363 |
| CSRP2 | 207030_s_at | <0.001 | 1.524 |
| CUGBP2 | 202158_s_at | <0.001 | 1.537 |
| CYB561 | 209163_at | <0.001 | 1.27 |
| DAB2 | 201280_s_at | <0.001 | 2.385 |
| ECGF1 | 204858_s_at | <0.001 | 2.037 |
| EMILIN1 | 204163_at | <0.01 | 2.002 |
| ENG | 201809_s_at | <0.001 | 1.441 |
| HIF1A | 200989_at | <0.001 | 1.981 |
| IFI30 | 201422_at | <0.001 | 1.886 |
| JAG1 | 209098_s_at | <0.001 | 1.458 |
| KDELR2 | 200699_at | <0.001 | 1.361 |
| LOX | 215446_s_at | <0.001 | 2.516 |
| LOXL1 | 203570_at | <0.001 | 2.013 |
| LOXL2 | 202998_s_at | <0.001 | 1.744 |
| LTBP3 | 219922_s_at | <0.001 | 1.507 |
| PGCP | 208454_s_at | <0.01 | 1.237 |
| PGRMC1 | 201121_s_at | <0.001 | 1.495 |
| PLOD2 | 202620_s_at | <0.001 | 1.725 |
| PLS3 | 201215_at | <0.001 | 1.59 |
| RASSF1 | 204346_s_at | <0.05 | −1.163 |
| RSU1 | 201980_s_at | <0.001 | 1.522 |
| S100A11 | 200660_at | <0.001 | 2.888 |
| SDC2 | 212158_at | 0.269 | 1.132 |
| SDC3 | 202898_at | <0.001 | 2.136 |
| SDCBP | 200958_s_at | <0.001 | 1.408 |
| SERPINH1 | 207714_s_at | <0.001 | 1.73 |
| SPARC | 200665_s_at | <0.001 | 2.205 |
| TAX1BP3 | 209154_at | <0.001 | 1.64 |
| TBCD | 211052_s_at | <0.001 | 1.581 |
| TGFB1 | 203085_s_at | <0.001 | 2.626 |
| TGFBI | 201506_at | <0.001 | 1.852 |
| TGFBR2 | 208944_at | <0.001 | 1.852 |
| TGFBR3 | 204731_at | 0.065 | 1.213 |
| TPM4 | 209344_at | <0.001 | 2.086 |
| TUBB2A | 204141_at | <0.001 | 2.16 |
List of the 56 transcript genes in the TGF-β network (Fig. 1 A) and their fold changes and p-values of t test for testing the significance of their changes between two groups: up-regulated group (DMD, JDM, and ED-D) and down-regulated group (FSH, NHM, and ALS). The results shown were from the data processed with PLIER. Those few transcripts showing nonsignificant p-values here are included, as they met significance thresholds with dCHIP mismatch probe set algorithm (not depicted).