Table 2 |
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|
Sample data subjected to permutation analysis or comparison by gene symbol instead of probe ID |
|||||||||
|
10% Data permutation (10,891 trials) |
Comparison by gene symbol |
||||||||
|
|
|||||||||
|
Name of L2L database list |
Binomial p value (actual) |
Median permutation 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 |
Total gene symbols on list |
Expected matches |
Actual matches |
Binomial p value |
|
|
|||||||||
|
ifn_beta_up |
1.9E-14 |
4.7E-12 |
0.10 |
3.2E-03 |
0.58 |
93 |
4.46 |
25 |
1.3E-12 |
|
ifn_alpha_up |
2.7E-14 |
1.4E-12 |
0.11 |
3.5E-03 |
0.31 |
71 |
3.41 |
22 |
1.2E-12 |
|
ifn_all_up |
2.0E-10 |
1.1E-08 |
0.20 |
0.011 |
0.80 |
48 |
2.30 |
14 |
3.5E-08 |
|
nf90_up |
3.1E-10 |
2.7E-09 |
0.21 |
0.012 |
0.70 |
37 |
1.78 |
11 |
8.3E-07 |
|
ifnalpha_both_up |
1.6E-09 |
2.0E-08 |
0.28 |
0.014 |
0.70 |
21 |
1.01 |
8 |
3.3E-06 |
|
adip_diff_cluster2 |
1.8E-07 |
1.5E-06 |
0.32 |
0.019 |
0.86 |
30 |
1.44 |
9 |
7.7E-06 |
|
emt_up |
5.1E-07 |
2.4E-06 |
0.25 |
0.021 |
0.84 |
68 |
3.26 |
11 |
3.8E-04 |
|
hpv31_dn |
1.3E-06 |
7.2E-06 |
0.30 |
0.022 |
0.79 |
49 |
2.35 |
9 |
4.8E-04 |
|
ifnalpha_either_up |
2.5E-06 |
1.2E-05 |
0.30 |
0.025 |
0.83 |
50 |
2.40 |
9 |
5.6E-04 |
|
adip_vs_fibro_up |
3.2E-06 |
2.0E-05 |
0.34 |
0.027 |
0.79 |
35 |
1.68 |
4 |
0.085 |
|
hypoxia_normal_up |
8.3E-06 |
6.3E-05 |
0.24 |
0.030 |
0.77 |
168 |
8.06 |
23 |
6.5E-06 |
|
hypoxia_reg |
8.5E-06 |
4.7E-05 |
0.35 |
0.031 |
0.74 |
39 |
1.87 |
9 |
7.7E-05 |
|
tnfalpha_adip_up |
5.3E-05 |
5.3E-05 |
0.54 |
0.048 |
0.75 |
8 |
0.38 |
1 |
0.33 |
|
cmv_up |
1.0E-04 |
4.1E-04 |
0.37 |
0.056 |
0.74 |
59 |
2.83 |
11 |
1.0E-04 |
|
vhl_normal_up |
1.8E-04 |
4.6E-04 |
0.31 |
0.065 |
0.78 |
155 |
7.44 |
19 |
1.8E-04 |
|
dsrna_up |
1.9E-04 |
9.7E-04 |
0.45 |
0.068 |
0.75 |
33 |
1.58 |
8 |
1.3E-04 |
|
tnfalpha_tgz_adip_up |
3.5E-04 |
3.5E-04 |
0.54 |
0.079 |
0.78 |
11 |
0.53 |
1 |
0.42 |
|
tgz_adip_up |
7.1E-04 |
7.1E-04 |
0.55 |
0.093 |
0.77 |
14 |
0.67 |
1 |
0.50 |
|
hif1_targets |
1.0E-03 |
4.2E-03 |
0.46 |
0.10 |
0.80 |
34 |
1.63 |
6 |
5.2E-03 |
|
adip_vs_preadip_up |
1.9E-03 |
7.6E-03 |
0.49 |
0.12 |
0.80 |
35 |
1.68 |
3 |
0.24 |
|
serum_fibroblast_core_dn |
5.1E-03 |
0.012 |
0.42 |
0.16 |
0.87 |
114 |
5.47 |
9 |
0.098 |
|
hypoxia_fibro_up |
7.5E-03 |
7.5E-03 |
0.62 |
0.17 |
0.86 |
22 |
1.06 |
3 |
0.086 |
|
|
|||||||||
|
Newman and Weiner Genome Biology 2005 6:R81 doi:10.1186/gb-2005-6-9-r81 |
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