Table 2.
Number of tests with p-values < 10-6, 10-7, 10-8
| No. p-Values below thresholda (permutation p-value) | ||||||||
|---|---|---|---|---|---|---|---|---|
| SNP set | Source | RA gene included in set | No. genes in set | Testb | N tests | <10-6 | <10-7 | <10-8 |
| Small cell lung cancer | KEGG | TRAF1 | 87 | Main effects | 3,429 | 6 (<0.001) | 6 (<0.001) | 3 (<0.001) |
| Interaction | 5,800,955 | 8 (0.081) | 0 (1) | 0 (1) | ||||
| JAK-STAT signaling pathway | KEGG | STAT4 | 153 | Main effects | 3,253 | 0 (1) | 0 (1) | 0 (1) |
| Interaction | 5,169,188 | 7 (0.137) | 3 (0.029) | 0 (1) | ||||
| Protein complex assembly | GO | TRAF1 | 214 | Main effects | 3,883 | 6 (<0.001) | 6 (<0.001) | 3 (<0.001) |
| Interaction | 7,277,905 | 292 (0.642) | 193 (0.152) | 151 (0.012) | ||||
| Protein amino acid dephosphorylation | GO | PTPN22 | 73 | Main effects | 2,277 | 0 (1) | 0 (1) | 0 (1) |
| Interaction | 2,496,978 | 1 (0.735) | 0 (1) | 0 (1) | ||||
| JAK-STAT cascade | GO | STAT4 | 41 | Main effects | 761 | 0 (1) | 0 (1) | 0 (1) |
| Interaction | 289,031 | 0 (1) | 0 (1) | 0 (1) | ||||
| Activation of MAPK activity | GO | C5 | 47 | Main effects | 785 | 3 (<0.001) | 3 (<0.001) | 1 (<0.001) |
| Interaction | 307,355 | 0 (1) | 0 (1) | 0 (1) | ||||
| Chemotaxis | GO | C5 | 112 | Main effects | 1,470 | 3 (<0.001) | 3 (<0.001) | 1 (<0.001) |
| Interaction | 1,065,328 | 1 (0.467) | 0 (1) | 0 (1) | ||||
| Inflammatory response | GO | C5 | 180 | Main effects | 2,535 | 3 (<0.001) | 3 (<0.001) | 1 (<0.001) |
| Interaction | 3,163,945 | 8 (0.025) | 0 (1) | 0 (1) | ||||
aEmpirical significance was determined by comparing the number of p-values below each threshold to a null distribution of the number obtained by permuting the phenotypes and performing main effects and interaction tests with the permuted data set.
bInteraction tests are unadjusted.