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Table 1 Sample data subjected to p value adjustment by Bonferroni correction or random-data simulation

From: L2L: a simple tool for discovering the hidden significance in microarray expression data

 

Actual diabetic nephropathy (downregulated) data

Random-data simulation (10,891 trials)

Name of L2L database list

Total U95Av2 probes on list

Expected matches

Actual matches

Binomial p value

Hypergeometric p value

Poisson p value

Bonferroni-adjusted binomial p value

Median binomial p value

p value (list-specific) of actual binomial p value

p value (all lists) of actual binomial p value

FDR of actual binomial p value

ifn_beta_up

135

5.83

31

1.9E-14

n/a

4.3E-14

6.7E-12

0.53

<9.2E-05

<2.6E-07

<9.2E-06

ifn_alpha_up

111

4.79

28

2.7E-14

1.4E-14

6.1E-14

9.5E-12

0.52

<9.2E-05

<2.6E-07

<9.2E-06

ifn_all_up

73

3.15

19

2.0E-10

1.4E-10

1.9E-10

7.0E-08

0.61

<9.2E-05

<2.6E-07

<9.2E-06

nf90_up

59

2.55

17

3.1E-10

2.3E-10

2.9E-10

1.1E-07

0.73

<9.2E-05

<2.6E-07

<9.2E-06

ifnalpha_both_up

36

1.55

13

1.6E-09

1.3E-09

1.3E-09

5.9E-07

0.80

<9.2E-05

<2.6E-07

<9.2E-06

adip_diff_cluster2

43

1.86

12

1.8E-07

1.5E-07

9.0E-08

6.6E-05

0.56

<9.2E-05

<2.6E-07

<9.2E-06

emt_up

104

4.49

18

5.1E-07

3.4E-07

2.9E-07

1.8E-04

0.66

<9.2E-05

<2.6E-07

<9.2E-06

hpv31_dn

69

2.98

14

1.3E-06

9.6E-07

6.2E-07

4.6E-04

0.58

<9.2E-05

2.6E-07

9.2E-06

ifnalpha_either_up

83

3.58

15

2.5E-06

1.8E-06

1.2E-06

9.0E-04

0.70

<9.2E-05

1.3E-06

4.2E-05

adip_vs_fibro_up

55

2.38

12

3.2E-06

2.5E-06

1.4E-06

1.2E-03

0.69

<9.2E-05

1.5E-06

4.6E-05

hypoxia_normal_up

243

10.49

27

8.3E-06

n/a

5.5E-06

3.0E-03

0.60

9.2E-05

3.9E-06

9.8E-05

hypoxia_reg

60

2.59

12

8.5E-06

6.5E-06

3.5E-06

3.0E-03

0.74

<9.2E-05

4.4E-06

9.8E-05

tnfalpha_adip_up

17

0.73

6

5.3E-05

4.8E-05

1.2E-05

0.019

0.53

<9.2E-05

2.2E-05

3.4E-04

cmv_up

88

3.80

13

1.0E-04

7.4E-05

4.5E-05

0.037

0.53

<9.2E-05

3.8E-05

5.1E-04

vhl_normal_up

230

9.93

23

1.8E-04

n/a

1.1E-04

0.066

0.53

1.8E-04

6.9E-05

7.9E-04

dsrna_up

48

2.07

9

1.9E-04

1.5E-04

6.2E-05

0.068

0.62

2.8E-04

7.4E-05

8.2E-04

tnfalpha_tgz_adip_up

23

0.99

6

3.5E-04

3.0E-04

8.0E-05

0.12

0.64

5.5E-04

1.5E-04

1.4E-03

tgz_adip_up

26

1.12

6

7.1E-04

6.1E-04

1.7E-04

0.25

0.68

5.5E-04

2.9E-04

2.4E-03

hif1_targets

60

2.59

9

1.0E-03

7.9E-04

3.7E-04

0.37

0.74

6.4E-04

4.5E-04

3.6E-03

adip_vs_preadip_up

53

2.29

8

1.9E-03

1.4E-03

6.2E-04

0.67

0.67

1.7E-03

9.3E-04

6.2E-03

serum_fibroblast_core_dn

148

6.39

14

5.1E-03

n/a

2.5E-03

1

0.62

4.2E-03

2.4E-03

0.013

hypoxia_fibro_up

29

1.25

5

7.5E-03

6.1E-03

1.9E-03

1

0.72

7.3E-03

3.5E-03

0.018

  1. n/a, calculation too complex to perform precisely.
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Genome Biology

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