Table 1. Comparison of the power to detect cis-acting regulatory SNPs using allele-specific expression (ASE) and genotype expression (GTE) analysis.
| Type of p-value threshold | Method | Number of samplesa | |||
| 395 | 188 | 95 | 50 | ||
| Total number of significant SNP-transcript associations | |||||
| FDR 5% | ASE | NA | 203893 | 127990 | 65258 |
| GTE | 31963 | 16757 | 6879 | 2077 | |
| ASE/GTE | NA | 12.2 | 18.6 | 31.4 | |
| FDR 1% | ASE | NA | 155205 | 87523 | 38685 |
| GTE | 22651 | 11101 | 4242 | 1151 | |
| ASE/GTE | NA | 14.0 | 20.6 | 33.6 | |
| Bonferroni correction pcorr = 0.05 | ASE | NA | 58078 | 23213 | 6781 |
| GTE | 9424 | 4277 | 1439 | 390 | |
| ASE/GTE | NA | 13.6 | 16.1 | 17.4 | |
| Bonferroni correction pcorr = 0.01 | ASE | NA | 51383 | 19357 | 5191 |
| GTE | 8337 | 3677 | 1189 | 300 | |
| ASE/GTE | NA | 14.0 | 16.3 | 17.3 | |
| Total number of significantly associated SNPs | |||||
| FDR 5% | ASE | NA | 111978 | 76161 | 42100 |
| GTE | 24379 | 13479 | 5887 | 1863 | |
| ASE/GTE | NA | 8.3 | 12.9 | 22.6 | |
| FDR 1% | ASE | NA | 88837 | 54758 | 26284 |
| GTE | 17975 | 9281 | 3739 | 1064 | |
| ASE/GTE | NA | 9.6 | 14.6 | 24.7 | |
| Bonferroni correction pcorr = 0.05 | ASE | NA | 37995 | 16467 | 5037 |
| GTE | 8148 | 3855 | 1349 | 370 | |
| ASE/GTE | NA | 9.9 | 12.2 | 13.6 | |
| Bonferroni correction pcorr = 0.01 | ASE | NA | 34131 | 13876 | 3881 |
| GTE | 7266 | 3335 | 1119 | 284 | |
| ASE/GTE | NA | 10.2 | 12.4 | 13.7 | |
| Total number of transcripts with significant SNP associations | |||||
| FDR 5% | ASE | NA | 12389 | 7111 | 6447 |
| GTE | 5051 | 3364 | 1850 | 740 | |
| ASE/GTE | NA | 3.7 | 3.8 | 8.7 | |
| FDR 1% | ASE | NA | 11914 | 6788 | 5472 |
| GTE | 3620 | 2256 | 1158 | 423 | |
| ASE/GTE | NA | 5.3 | 5.9 | 12.9 | |
| Bonferroni correction pcorr = 0.05 | ASE | NA | 8723 | 4395 | 1984 |
| GTE | 1867 | 1064 | 476 | 165 | |
| ASE/GTE | NA | 8.2 | 9.2 | 12.0 | |
| Bonferroni correction pcorr = 0.01 | ASE | NA | 8223 | 3994 | 1607 |
| GTE | 1712 | 948 | 407 | 133 | |
| ASE/GTE | NA | 8.7 | 9.8 | 12.1 | |
a
Median values of 10 runs for the random sample subsets. The top panel show the number of significant SNP-transcript associations, the middle panel show the number of significantly associated SNPs when counting only the best SNP-transcript association for each SNP, and the bottom panel show the number of transcripts that have at least one significantly associated SNP. Both the Bonferroni and FDR p-value thresholds are used. ASE/GTE = Ratio between number of significant ASE and GTE associations.