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Table 1 List of the highest up-regulated genes in the gene array after rotenone treatment

From: Vascular endothelial growth factor B (VEGF-B) is up-regulated and exogenous VEGF-B is neuroprotective in a culture model of Parkinson's disease

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
  1. 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.