Table 2.
Ability to Recover Disease Subnetworks Comprising Three Genes
| Intersection filtering | HetRank | |||||
|---|---|---|---|---|---|---|
| Gene 1 | Gene 2 | Gene 3 | Gene 1 | Gene 2 | Gene 3 | |
| (a) | Number of 1000 simulations achieving given ranking using high‐coverage disease subnetworks | |||||
| Autosomal dominant mode | ||||||
| Ranked #1 | 293 | 402 | ||||
| Ranked #1–2 | |‐ ‐ ‐ ‐ ‐ ‐ 42 ‐ ‐ ‐ ‐ ‐ ‐| | |‐ ‐ ‐ ‐ ‐ ‐ 201 ‐ ‐ ‐ ‐ ‐ ‐| | ||||
| Ranked #1–3 | |‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ 3 ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐| | |‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ 79 ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐| | ||||
| Ranked ≤10 | 590 | 156 | 16 | 649 | 447 | 214 |
| Ranked ≤100 | 787 | 345 | 58 | 838 | 711 | 506 |
| Median rank | 3 | 189 | 10,000 | 3 | 16 | 95.5 |
| Autosomal recessive mode | ||||||
| Ranked #1 | 500 | 901 | ||||
| Ranked #1–2 | |‐ ‐ ‐ ‐ ‐ ‐ 124 ‐ ‐ ‐ ‐ ‐ ‐| | |‐ ‐ ‐ ‐ ‐ ‐ 769 ‐ ‐ ‐ ‐ ‐ ‐| | ||||
| Ranked #1–3 | |‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ 10 ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐| | |‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ 398 ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐| | ||||
| Ranked ≤10 | 905 | 504 | 82 | 964 | 911 | 733 |
| Ranked ≤100 | 985 | 830 | 317 | 993 | 976 | 925 |
| Median rank | 1.25 | 8 | 243 | 1 | 2 | 4 |
| Neutral mode | ||||||
| Ranked #1 | 342 | 425 | ||||
| Ranked #1–2 | |‐ ‐ ‐ ‐ ‐ ‐ 54 ‐ ‐ ‐ ‐ ‐ ‐| | |‐ ‐ ‐ ‐ ‐ ‐ 229 ‐ ‐ ‐ ‐ ‐ ‐| | ||||
| Ranked #1–3 | |‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ 5 ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐| | |‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ 83 ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐| | ||||
| Ranked ≤10 | 618 | 168 | 20 | 664 | 468 | 236 |
| Ranked ≤100 | 804 | 361 | 73 | 845 | 725 | 523 |
| Median rank | 2.5 | 188.5 | 10,000 | 2 | 13 | 88 |
| (b) | Number of 1000 simulations achieving given ranking using low‐coverage disease subnetworks | |||||
| Autosomal dominant mode | ||||||
| Ranked #1 | 299 | 368 | ||||
| Ranked #1–2 | |‐ ‐ ‐ ‐ ‐ ‐ 31 ‐ ‐ ‐ ‐ ‐ ‐| | |‐ ‐ ‐ ‐ ‐ ‐ 124 ‐ ‐ ‐ ‐ ‐ ‐| | ||||
| Ranked #1–3 | |‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ 1 ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐| | |‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ 36 ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐| | ||||
| Ranked ≤10 | 601 | 150 | 5 | 595 | 312 | 115 |
| Ranked ≤100 | 772 | 348 | 52 | 803 | 573 | 293 |
| Median rank | 3.5 | 195 | 10,000 | 4 | 56 | 456 |
| Autosomal recessive mode | ||||||
| Ranked #1 | 496 | 852 | ||||
| Ranked #1–2 | |‐ ‐ ‐ ‐ ‐ ‐ 138 ‐ ‐ ‐ ‐ ‐ ‐| | |‐ ‐ ‐ ‐ ‐ ‐ 567 ‐ ‐ ‐ ‐ ‐ ‐| | ||||
| Ranked #1–3 | |‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ 11 ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐| | |‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ 209 ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐| | ||||
| Ranked ≤10 | 896 | 492 | 78 | 945 | 791 | 473 |
| Ranked ≤100 | 987 | 817 | 333 | 989 | 931 | 700 |
| Median rank | 1.5 | 16 | 237 | 1 | 2 | 14 |
| Neutral mode | ||||||
| Ranked #1 | 329 | 377 | ||||
| Ranked #1–2 | |‐ ‐ ‐ ‐ ‐ ‐ 37 ‐ ‐ ‐ ‐ ‐ ‐| | |‐ ‐ ‐ ‐ ‐ ‐ 139 ‐ ‐ ‐ ‐ ‐ ‐| | ||||
| Ranked #1–3 | |‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ 1 ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐| | |‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ 40 ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐| | ||||
| Ranked ≤10 | 632 | 173 | 11 | 620 | 343 | 128 |
| Ranked ≤100 | 779 | 366 | 64 | 822 | 597 | 312 |
| Median rank | 3 | 188.75 | 10,000 | 3 | 43.5 | 424.5 |
For all tests: uncaptured heterogeneity u = 0.5; captured heterogeneity split equally between the three genes (p 1 = p 2 = p 3). Intersection filtering = results obtained using ranking based on intersection filtering; HetRank = results obtained using HetRank approach with interaction data from PINAmin2 network; Gene 1 = highest‐ranked of three disease genes in results; Gene 2 = second‐highest ranked; Gene 3 = lowest ranked. (a) Results using high‐coverage disease subnetworks (identified in PINAmin2 network). (b) Results using low‐coverage disease subnetworks (identified in PINA network).