Table 3.
Likelihood ratio test (LRT) results comparing full models (consisting of all SNPs for the gene) and null models after controlling for HIV infection.
| Not controlling for HIV | Controlling for HIV | ||||
|---|---|---|---|---|---|
| Gene name | LRT p value | 5% significance threshold∗ | Gene name | LRT p value | 5% significance threshold∗ |
| HLA-DQB1 | 1.76∗10−5 | 0.0006 | HLA-DQB1 | 1.84∗10−5 | 0.0005 |
| IL-6 | 0.0007 | 0.0117 | IL-6 | 0.0008 | 0.0110 |
| IL-28B | 0.1700 | 0.0347 | IL28B | 0.1600 | 0.0324 |
| IL-10 | 0.1987 | 0.0697 | IL-10 | 0.2603 | 0.0645 |
| CTLA-4 | 0.4514 | 0.1124 | CTLA4 | 0.4305 | 0.1059 |
| HLA-DRB1 | 0.4981 | 0.1661 | HLA-DRB1 | 0.4759 | 0.1602 |
| SOCS1 | 0.5313 | 0.2264 | SOCS1 | 0.5071 | 0.2195 |
| TNF | 0.6957 | 0.2952 | TNF | 0.6508 | 0.2888 |
| IFNG | 0.7391 | 0.3755 | SOCS3 | 0.7475 | 0.3675 |
| TGF-beta-1 | 0.7590 | 0.4677 | TGF-beta-1 | 0.8025 | 0.4548 |
| SOCS3 | 0.7742 | 0.5738 | IFNG | 0.8027 | 0.5630 |
| IL-18 | 0.9567 | 0.7027 | IL-18 | 0.9649 | 0.7037 |
∗5% significance thresholds derived from permutation distributions (unstratified). A gene reaches statistical significance under the step-down procedure when the observed LRT p values for it and all more significant genes are less than their corresponding 5% thresholds.