Table 2.
A comparison of the results from different methods when applied to the ISG gene list
| Abstract term | Chip | List |
Bonferroni P-value |
||
|---|---|---|---|---|---|
| Permutation | Outlier | ExtendedHG | |||
| INTERFERON | 414 | 46 | <0.0484 | 9.81 × 10−34 | 2.12 × 10−31 |
| IFN | 245 | 35 | <0.0484 | 8.90 × 10−19 | 1.35 × 10−25 |
| IFN-BETA | 71 | 18 | <0.0484 | 5.60 × 10−11 | 1.34 × 10−14 |
| ANTIVIRAL | 176 | 23 | <0.0484 | 2.24 × 10−8 | 1.03 × 10−13 |
| IFN-ALPHA | 114 | 19 | <0.0484 | 3.00 × 10−8 | 2.49 × 10−12 |
| INTERFERON-ALPHA | 59 | 14 | <0.0484 | 6.08 × 10−8 | 5.85 × 10−10 |
| OLIGOADENYLATE | 18 | 8 | <0.0484 | 2.26 × 10−6 | 8.29 × 10−6 |
| ISG | 14 | 7 | <0.0484 | 1.41 × 10−5 | 9.05 × 10−5 |
| ISRE | 31 | 9 | <0.0484 | 2.06 × 10−5 | 1.62 × 10−5 |
| DSRNA | 60 | 11 | <0.0484 | 0.0001 | 1.03 × 10−5 |
| HLA-CLASS | 11 | 6 | <0.0484 | 0.0002 | 0.0015 |
| HLA-A | 30 | 8 | 1 | 0.0003 | 0.0005 |
| HLA-B | 25 | 7 | 1 | 0.0024 | 0.0048 |
| INDUCIBLE | 1068 | 37 | <0.0484 | 0.0025 | 1.29 × 10−7 |
| ENCEPHALOMYOCARDITIS | 16 | 6 | <0.0484 | 0.0036 | 0.0136 |
| STOMATITIS | 52 | 9 | <0.0484 | 0.0036 | 0.0013 |
| OAS | 10 | 5 | 0.0968 | 0.0145 | 0.1047 |
| HLA-G | 10 | 5 | 1 | 0.0145 | 0.1047 |
| MXA | 11 | 5 | 1 | 0.0257 | 0.1624 |
| EVASION | 65 | 9 | <0.0484 | 0.0258 | 0.0074 |
| INNATE | 363 | 21 | 0.0484 | 0.0311 | 1.35 × 10−5 |
| TAPASIN | 12 | 5 | 1 | 0.0427 | 0.2407 |
| VIRAL | 892 | 32 | 0.0484 | 0.0447 | 4.25 × 10−6 |
| INFECTION | 1177 | 36 | 0.0968 | 0.0477 | 9.61 × 10−6 |
| OR-C | 5 | 4 | <0.0484 | 0.0717 | 0.5133 |
| LYMPHOBLASTOID | 239 | 16 | <0.0484 | 0.0872 | 0.0004 |
| IFN-GAMMA | 443 | 22 | 0.1936 | 0.1113 | 6.38 × 10−5 |
| IMMUNITY | 387 | 20 | 0.0968 | 0.1799 | 0.0002 |
| IMMUNE | 1275 | 35 | 0.6776 | 0.4363 | 0.0003 |
| TREAT | 1817 | 40 | <0.0484 | 0.9165 | 0.0033 |
| MHC | 353 | 17 | 1 | 1 | 0.0115 |
| VIRUS | 1408 | 34 | 1 | 1 | 0.0089 |
Abstract terms that are identified as over-represented by the corresponding method are shown in bold. The cutoff used is P ≤ 0.05 after Bonferroni correction. 100 000 randomisations were performed for the permutation test. 4840 tokens were being tested during the permutation test and the best possible Bonferroni P-value attainable is 10–5 × 4840 = 0.0484. Any term with an empirical P-value less than 10–5 is provisionally assigned a value of <10–5, and the corresponding Bonferroni P-value is set to be <0.0484. The unadjusted P-values and other details (e.g. Z-scores and odds ratio) can be found in Supplementary Data 1, Table S1. Chip is the number of genes that contains a given term on the entire chip; List is the number of genes that are associated with a given term in the ISG gene list.