Table 7 RF-based prediction error rates of SNP sets from functional module-based filtration and SNP combinations with various thresholds from the WTCCC T2D dataset.
Dataset | Functional Module Description | Number of SNPs | Error Rate | Number of Selected SNPs | Error Rate with Variable Selection |
|---|---|---|---|---|---|
MIR | CACTGCC,MIR-34A, MIR-34C,MIR-449 | 1876 | 39.02% | 6 | 32.12% |
TF | V$NKX25_02 | 1678 | 38.56% | 59 | 33.06% |
MIR | ACTTTAT,MIR-142-5P | 1572 | 38.32% | 35 | 33.42% |
Average | Average of results from 66 functional modules | 1614.86 | 39.18% | 32.24 | 36.98% |
Random Average | Average of results from 66 SNP sets consisting of randomly selected 1615 SNPs | 1615 | 38.77% | 113.17 | 36.57% |
Combination | Top 5 functional modules | 7590 | 38.96% | 36 | 32.78% |
Combination | Top 66 functional modules | 25663 | 38.66% | 62 | 17.43% |
p-value based | Top 1 SNP | 1 | 33.93% | 1 | 33.93% |
p-value based | Top 10 SNPs | 10 | 27.19% | 10 | 27.19% |
p-value based | SNPs with Bonferroni threshold | 82 | 11.76% | 82 | 11.76% |
p-value based | SNPs with p-value < 0.01 | 854 | 14.79% | 114 | 11.70% |
p-value based | All SNPs | 42798 | 37.02% | 83 | 11.47% |