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Table 1 Comparison of RCMAT with the procedure of Kong et al.

From: RCMAT: a regularized covariance matrix approach to testing gene sets

Gene Set

No. of Genes in Set

RCMAT

p-value

Kong et al.

p-value

c25_U133_probes

64

0.0003

0.0039

MAP00600_Sphingoglycolipid_metabolism

18

0.0018

0.0036

MAP00300_Lysine_biosynthesis

5

0.002

0.0089

MAP00561_Glycerolipid_metabolism

84

0.0028

0.7803

c29_U133_probes

202

0.0033

0.0672

c33_U133_probes

362

0.0034

0.1201

c23_U133_probes

109

0.0035

0.1581

MAP00360_Phenylalanine_metabolism

23

0.0036

0.0723

MAP00531_Glycosaminoglycan_degradation

18

0.0043

0.0005

MAP00511_N_Glycan_degradation

9

0.0072

0.0066

GLUCO_HG-U133A_probes

46

0.0084

0.4585

GLYCOL_HG-U133A_probes

31

0.0088

0.5699

MAP00910_Nitrogen_metabolism

31

0.0094

0.0385

MAP00430_Taurine_and_hypotaurine_metabolism

12

0.01

0.0888

mitochondr_HG-U133A_probes

615

0.0107

0.05

MAP00650_Butanoate_metabolism

38

0.0109

0.3458

human_mitoDB_6_2002_HG-U133A_probes

594

0.0113

0.0381

c28_U133_probes

288

0.0123

0.1947

MAP00252_Alanine_and_aspartate_metabolism

35

0.0131

0.0472

c20_U133_probes

270

0.0139

0.1125

MAP00190_Oxidative_phosphorylation

75

0.0141

0.2173

c22_U133_probes

194

0.0152

0.016

MAP00710_Carbon_fixation

27

0.0152

0.0297

MAP00340_Histidine_metabolism

32

0.0154

0.2045

MAP00330_Arginine_and_proline_metabolism

63

0.0168

0.0062

c31_U133_probes

346

0.0172

0.3197

MAP00380_Tryptophan_metabolism

88

0.018

0.7238

MAP00380_Tryptophan_metabolism~

88

0.0195

0.7156

c7_U133_probes

349

0.0207

0.1292

c15_U133_probes

264

0.0232

0.4323

MAP00512_O_Glycans_biosynthesis

15

0.0236

0.0322

MAP00970_Aminoacyl_tRNA_biosynthesis

34

0.024

0.1054

c27_U133_probes

266

0.0253

0.1722

MAP00251_Glutamate_metabolism

35

0.0256

0.0259

c12_U133_probes

251

0.0263

0.087

MAP00031_Inositol_metabolism

7

0.0265

0.0677

MAP00410_beta_Alanine_metabolism

27

0.0291

0.5854

c34_U133_probes

452

0.0311

0.2366

c11_U133_probes

192

0.0334

0.4341

c18_U133_probes

248

0.0335

0.0167

MAP00590_Prostaglandin_and_leukotriene_metabolism

34

0.0348

0.1956

c14_U133_probes

302

0.0361

0.1327

c35_U133_probes

470

0.0419

0.2794

OXPHOS_HG-U133A_probes

114

0.0441

0.1705

ROS_HG-U133A_probes

9

0.0446

0.1523

c3_U133_probes

267

0.0455

0.5362

c30_U133_probes

239

0.0462

0.1006

GO_0005739_HG-U133A_probes

227

0.0467

0.3106

MAP00310_Lysine_degradation

35

0.0477

0.4446

FA_HG-U133A_probes

34

0.0485

0.1047

  1. For each of the gene sets from Mootha et al. [3] both the RCMAT and the method of Kong et al. were applied. Nominal (unadjusted) permutation p-values for each of the two procedures are given. The number of genes in the pathway is also provided.
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BMC Bioinformatics

ISSN: 1471-2105

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