Table 1.
List of the highest up-regulated genes in the gene array after rotenone treatment
| gene_id | ID | adj. P value | B value |
| Atf5 | NM_172336 | 3.39E-05 | 9.733544 |
| RGD1561519_predicted | NM_001109112 | 0.003306 | 6.712279 |
| Asns | U07201 | 0.003466 | 6.388728 |
| LOC690315 | NM_001109577 | 0.004486 | 5.986556 |
| Slc7a5 | NM_017353 | 0.006186 | 5.572276 |
| Sdf2l1_predicted | NM_001109433 | 0.007716 | 5.109109 |
| Lce1s_predicted | XM_001066389 | 0.007716 | 5.029038 |
| Slc7a3 | NM_017217 | 0.0086 | 4.713449 |
| Klhl6_predicted | NM_001105867 | 0.0086 | 4.684208 |
| Ns5atp9 | NM_201418 | 0.008757 | 4.59833 |
| Mrc1_predicted | NM_001106123 | 0.009356 | 4.427766 |
| Lrrc33 | NM_001024995 | 0.009356 | 4.41691 |
| LOC290651 | NM_001013880 | 0.010522 | 4.201058 |
| Pycs_predicted | NM_001108524 | 0.010522 | 4.140525 |
| Vegfb | NM_053549 | 0.010522 | 4.090442 |
| Shmt2 | NM_001008322 | 0.010522 | 4.077214 |
| Ncf1 | NM_053734 | 0.010522 | 4.063953 |
| Aldh1l2_predicted | XM_235005 | 0.01345 | 3.812624 |
| Mmp9 | NM_031055 | 0.015332 | 3.603003 |
| Dnajc3 | NM_022232 | 0.015332 | 3.583457 |
| Dpp7 | NM_031973 | 0.015332 | 3.516206 |
| Hmgcr | NM_013134 | 0.015332 | 3.509113 |
| Gpnmb | NM_133298 | 0.015786 | 3.39472 |
| Cndp2 | NM_001010920 | 0.015786 | 3.37061 |
| Pcp4 | M24852 | 0.015786 | 3.355451 |
| LOC680308 | NM_001109398 | 0.016276 | 3.29948 |
| Txnip | NM_001008767 | 0.017441 | 3.210653 |
| Eprs | NM_001024238 | 0.018104 | 3.150337 |
| Tm6sf1_predicted | NM_001108490 | 0.019731 | 3.047957 |
| Calr | NM_022399 | 0.020863 | 2.959711 |
| RGD1564553_predicted | XM_577290 | 0.021343 | 2.854501 |
| Yars | NM_001025696 | 0.02214 | 2.778994 |
| RGD1564228_predicted | XM_001081442 | 0.02214 | 2.776624 |
| Igf1 | NM_178866 | 0.022922 | 2.701602 |
| Hexb | NM_001011946 | 0.022922 | 2.681626 |
| Myo1f_predicted | NM_001108076 | 0.023081 | 2.655012 |
| Cd180_predicted | NM_001106405 | 0.024702 | 2.574536 |
| Cd68 | NM_001031638 | 0.025665 | 2.501227 |
List of the top 38 up-regulated genes in the gene array after rotenone treatment (genes with significance values of both the adjusted P ≤ 0.025 and the false discovery rate log-odds score B>2.5 were included in the Table; n = 3 separate experiments). The P value is based upon a t test of the average ratio of expression values for the treated and untreated samples and adjusted for multiple testing using the false discovery rate, as implemented in the Bioconductor limma library http://www.bioconductor.org. B is the false discovery rate expressed as a log odds score, so B = 3 means that there is 5% chance of being incorrect. VEGF-B is ranked 15th highest, and the B = 4.09 correlates to >98% chance that treatment is different form control. MMP9 is ranked 19th, and the B value = 3.60 correlates to >97% chance that treatment is different form control.