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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.
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Molecular Neurodegeneration

ISSN: 1750-1326