Table 2 Sample data subjected to permutation analysis or comparison by gene symbol instead of probe ID
From: L2L: a simple tool for discovering the hidden significance in microarray expression data
| Â | 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 |