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Table 1 Significantly expressed proteins - ANOVA result

From: A guide through the computational analysis of isotope-labeled mass spectrometry-based quantitative proteomics data: an application study

Accession

ANOVA

adjusted p-values

Fligner-Killeen

adjusted p-values

Shapiro-Wilks

adjusted p-values

Kruskal-Wallis

adjusted p-values

Number of identified

peptide hits

P40780

<0.000001

>0.99

>0.99

<0.000001

741

O34833

<0.000001

0.007364

<0.000001

0.000001

827

O32076

<0.000001

0.000083

>0.99

<0.000001

1344

O34538

<0.000001

0.000020

0.977644

<0.000001

1616

P94565

<0.000001

>0.99

0.264667

0.000003

1033

P54466

<0.000001

0.003793

<0.000001

<0.000001

2382

P33166

<0.000001

<0.000001

0.067524

<0.000001

1605

P02968

<0.000001

0.000001

<0.000001

<0.000001

9369

P37809

<0.000001

0.000002

0.007523

<0.000001

1112

P46920

<0.000001

>0.99

<0.000001

<0.000001

1149

P09124

<0.000001

>0.99

>0.99

<0.000001

685

P35136

<0.000001

>0.99

0.000003

<0.000001

1498

P37808

<0.000001

>0.99

>0.99

<0.000001

1219

P94356

<0.000001

0.037934

0.414572

<0.000001

2053

P80877

<0.000001

>0.99

>0.99

0.000002

892

P27206

<0.000001

0.000004

0.000028

<0.000001

2232

P37871

<0.000001

0.399160

0.901907

<0.000001

1938

O34992

<0.000001

0.085647

<0.000001

<0.000001

1215

P37476

<0.000001

>0.99

<0.000001

<0.000001

3203

Q04747

<0.000001

<0.000001

0.000199

<0.000001

3460

O31709

<0.000001

>0.99

>0.99

0.000020

295

P35149

<0.000001

0.000169

>0.99

0.000693

751

P08065

<0.000001

0.328408

<0.000001

<0.000001

2140

P19582

<0.000001

>0.99

0.011528

0.000008

903

O34966

<0.000001

0.012613

0.000188

<0.000001

1837

P08750

<0.000001

>0.99

<0.000001

<0.000001

1109

O34442

<0.000001

>0.99

0.047638

0.000552

291

P24141

0.000001

>0.99

<0.000001

<0.000001

1257

P25994

0.000001

0.755894

0.006728

0.000072

1641

O32243

0.000003

0.599332

>0.99

0.000505

404

O06745

0.000005

>0.99

0.013199

0.011193

485

P37527

0.000013

>0.99

>0.99

0.051621

181

P04969

0.000016

>0.99

>0.99

0.708837

745

O32167

0.000020

>0.99

0.001374

0.000021

2891

O32157

0.000035

0.016583

<0.000001

0.000796

957

O31501

0.000036

0.006965

<0.000001

<0.000001

1681

P20166

0.000046

0.272716

0.044373

0.000003

1948

P21471

0.000052

>0.99

>0.99

0.558509

130

P26906

0.000063

>0.99

>0.99

0.875231

300

P54535

0.000073

>0.99

<0.000001

<0.000001

2391

O31663

0.000143

>0.99

>0.99

0.378199

340

O34633

0.000185

>0.99

>0.99

0.025892

433

P09339

0.000203

0.244699

>0.99

0.040871

619

O07516

0.000230

>0.99

>0.99

0.955961

370

P24327

0.000234

>0.99

<0.000001

<0.000001

1692

P37494

0.000244

>0.99

>0.99

0.932235

241

P32399

0.000267

>0.99

>0.99

0.045315

388

P39912

0.000327

>0.99

>0.99

0.002252

878

P42971

0.000473

>0.99

>0.99

0.032372

475

P21472

0.000594

>0.99

>0.99

¿ 0.99

357

P21464

0.000613

>0.99

<0.000001

0.000473

1272

P71021

0.000703

>0.99

>0.99

¿ 0.99

173

O31567

0.001315

>0.99

0.000289

0.002616

613

O06491

0.001750

>0.99

>0.99

0.542278

268

O34789

0.001860

>0.99

>0.99

¿ 0.99

106

O35007

0.002474

>0.99

>0.99

0.011411

410

P71044

0.002703

>0.99

0.000005

0.000284

635

P12042

0.002703

>0.99

>0.99

0.043005

699

P46921

0.003377

>0.99

>0.99

0.421630

173

P28611

0.004644

>0.99

>0.99

0.193988

259

P13484

0.006385

>0.99

>0.99

¿ 0.99

208

P39215

0.006851

0.484875

>0.99

0.275825

608

O32218

0.009165

>0.99

>0.99

0.018027

567

P18185

0.011352

>0.99

>0.99

¿ 0.99

220

P21467

0.015346

>0.99

0.000001

0.001040

781

P37870

0.017921

0.000748

>0.99

0.041718

1113

O31657

0.018006

>0.99

>0.99

0.111378

227

O06478

0.022471

>0.99

>0.99

0.859843

229

O34878

0.022750

>0.99

>0.99

¿ 0.99

83

O32247

0.025031

>0.99

>0.99

0.028009

845

P39694

0.031255

>0.99

0.293920

¿ 0.99

96

P42319

0.038119

>0.99

>0.99

¿ 0.99

224

P49785

0.039250

>0.99

0.000245

0.002557

536

  1. Exemplary shown for experiment A, this table displays all ANOVA-reported significantly expressed proteins having a p-value below the acceptable significance level of p < 0.05 (further results can be found in the supplementary data). Proteins are sorted by the ANOVA's p-value in ascending order. The assumption that all values are derived from a normal distribution was investigated using a Shapiro-Wilks test: in 29 cases the normal distribution assumption was violated. To analyze the homogeneity of variances of each group a Fligner-Killeen test was performed. Here, 15 of the proteins showed inhomogeneous variances. In summary, only 38 proteins fulfilled all criteria (in bold print). Interestingly, 21 of these proteins were not found significantly regulated by a Kruskal-Wallis test (in italics). All computed p-values where corrected using the method described by Holm [33].