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Table 3 Variance component-based total effect test p-values for gene sets associated with lung cancer after Bonferroni correction

From: Integrated genomic analysis of biological gene sets with applications in lung cancer prognosis

   

Approximated P-Values

Empirical P-Values

Omnibus P-Values

 
 

N0

N T

Q MGC

Q MG

Q M

Q G

Q MGC

Q MG

Q M

Q G

iNOTE chi

iNOTE uni

GSAA

BRUECKNER TARGETS OF MIRLET7A3 DN

78

71

1.1E-05

1.7E-06

5.5E-04

2.4E-04

<1E-04

<1E-04

8E-04

3E-04

8E-04

<1E-04

0.325

BRUECKNER TARGETS OF MIRLET7A3 UP

111

106

1.3E-06

4.1E-07

2.5E-04

1.3E-04

<1E-04

<1E-04

4E-04

1E-04

2E-04

<1E-04

0.230

COLDREN GEFITINIB RESISTANCE DN

230

216

8.0E-09

3.2E-10

1.2E-09

8.9E-04

<1E-04

<1E-04

<1E-04

9E-04

<1E-04

<1E-04

0.095

DAUER STAT3 TARGETS UP

49

49

1.6E-04

4.6E-05

0.002

0.003

7E-04

2E-04

0.003

0.002

4E-04

3E-04

<1E-04

DCA UP.V1 DN

193

163

6.1E-06

4.9E-06

0.003

1.3E-04

<1E-04

<1E-04

0.004

<1E-04

<1E-04

<1E-04

0.920

DCA UP.V1 UP

191

162

7.3E-05

4.7E-05

0.002

0.003

1E-04

1E-04

0.002

0.004

<1E-04

<1E-04

0.065

HALMOS CEBPA TARGETS DN

46

44

2.4E-04

9.5E-05

0.018

5.4E-04

8E-04

<1E-04

0.021

4E-04

0.001

<1E-04

0.645

HATADA METHYLATED IN LUNG CANCER UP

390

356

9.3E-07

2.6E-07

2.8E-06

0.003

<1E-04

<1E-04

<1E-04

0.003

<1E-04

<1E-04

0.900

KIM MYC AMPLIFICATION TARGETS UP

201

169

2.2E-06

1.3E-06

0.004

2.9E-05

<1E-04

<1E-04

0.005

<1E-04

<1E-04

<1E-04

0.605

KOBAYASHI EGFR SIGNALING 24HR DN

251

228

7.3E-04

1.7E-05

9.6E-07

0.109

9E-04

<1E-04

<1E-04

0.110

0.015

<1E-04

0.920

KOBAYASHI EGFR SIGNALING 24HR UP

101

91

1.7E-09

1.9E-08

9.0E-04

3.2E-06

<1E-04

<1E-04

0.001

<1E-04

<1E-04

<1E-04

0.035

KOBAYASHI EGFR SIGNALING 6HR DN

18

18

5.4E-05

9.5E-06

2.5E-04

0.003

<1E-04

<1E-04

9E-04

0.004

<1E-04

<1E-04

0.110

KRAS.600.LUNG.BREAST UP.V1 DN

289

261

3.4E-04

3.4E-04

0.020

0.003

7E-04

2E-04

0.023

0.004

<1E-04

4E-04

0.125

KRAS.600.LUNG.BREAST UP.V1 UP

288

247

8.8E-07

2.3E-06

0.100

7.9E-07

<1E-04

<1E-04

0.105

<1E-04

<1E-04

<1E-04

0.060

KRAS.AMP.LUNG UP.V1 UP

144

121

9.0E-05

1.7E-04

0.288

1.6E-05

5E-04

4E-04

0.284

1E-04

<1E-04

<1E-04

0.045

KRAS.DF.V1 UP

193

175

3.3E-08

1.4E-08

3.1E-04

5.1E-06

<1E-04

<1E-04

4E-04

<1E-04

1E-04

<1E-04

0.160

KRAS.LUNG UP.V1 UP

141

126

5.3E-10

5.1E-09

0.025

1.1E-08

<1E-04

<1E-04

0.026

<1E-04

<1E-04

<1E-04

0.575

LI AMPLIFIED IN LUNG CANCER

178

165

1.6E-04

6.1E-05

9.5E-05

0.031

3E-04

1E-04

1E-04

0.032

0.009

<1E-04

0.180

LOCKWOOD AMPLIFIED IN LUNG CANCER

214

205

1.6E-04

6.7E-06

6.7E-07

0.081

2E-04

<1E-04

<1E-04

0.081

0.014

<1E-04

0.230

SHEDDEN LUNG CANCER GOOD SURVIVAL A12

317

269

7.9E-10

9.7E-09

0.003

1.4E-07

<1E-04

<1E-04

0.002

<1E-04

<1E-04

<1E-04

0.385

SHEDDEN LUNG CANCER GOOD SURVIVAL A4

196

186

6.0E-06

5.7E-06

5.7E-05

0.006

<1E-04

<1E-04

2E-04

0.007

<1E-04

<1E-04

0.470

SHEDDEN LUNG CANCER POOR SURVIVAL A6

456

411

2.2E-08

1.4E-11

8.1E-11

7.6E-04

<1E-04

<1E-04

<1E-04

0.001

1E-04

<1E-04

0.900

SWEET KRAS ONCOGENIC SIGNATURE

89

81

0.010

3.8E-04

3.1E-05

0.157

0.011

4E-04

<1E-04

0.158

0.019

<1E-04

0.180

SWEET KRAS TARGETS DN

66

59

3.1E-08

2.3E-09

5.0E-04

6.5E-07

<1E-04

<1E-04

0.001

<1E-04

<1E-04

<1E-04

0.655

TBK1.DF DN

287

266

2.9E-08

3.9E-09

1.3E-05

2.3E-05

<1E-04

<1E-04

<1E-04

<1E-04

5E-04

<1E-04

0.570

TBK1.DF UP

290

275

0.006

0.001

2.4E-04

0.174

0.008

0.002

2E-04

0.172

0.051

2E-04

0.265

TOOKER GEMCITABINE RESISTANCE DN

122

115

4.1E-05

1.1E-05

8.8E-05

0.006

<1E-04

<1E-04

2E-04

0.007

0.004

<1E-04

0.710

ZHONG RESPONSE TO AZACITIDINE AND TSA UP

183

158

1.1E-05

9.8E-07

3.0E-07

0.024

1E-04

<1E-04

<1E-04

0.025

1E-04

<1E-04

0.935

  1. Satterthwaite-approximated and empirical p-values for all significant gene sets after Bonferroni correction by at least one of the iTEGS and at least one of the iNOTE tests. Empirical p-values and approximated p-values are very similar, irrespective of the sizes of the gene sets tested. N0: total no. of genes in the gene set; N T : total no. of genes with methylation and gene expression data available (i.e. tested); Q: the iTEGS Q-statistic test specifying M, G, MG, or MGC; Bonferroni adjusted p-value threshold was calculated as α/M=5×10−04, where α=0.05 and M is the total number of gene sets tested
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BMC Bioinformatics

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