Table 3.
Probes and corresponding 44 genes selected by ML algorithms and penalized regression models for association between the genes with occurrence and progression of COPD. The effect of smoking (pack per year) was adjusted in all of the methods.
| Gene Symbol | Probe ID | Number of Methods | LASSO | Adapt. LASSO | Elastic net | Ridge | SVM | GBM | NB | RF | ANN | RT | ABCT | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1. | PPP4R4 | 233002_at | 3 | 80% | 78% | 96% | — | — | — | — | — | — | — | — |
| 2. | THSD4 | 222835_at | 2 | — | — | 90% | — | — | — | — | — | 43% | — | — |
| 3. | NRG1 | 206343_s_at | 3 | — | — | — | — | 55% | — | 55% | — | — | — | 65% |
| 4. | SCGB1A1 | 205725_at | 6 | — | — | 30% | 61% | 54% | — | 54% | — | 78% | — | 64% |
| 5. | AHRR | 229354_at | 8 | 98% | 96% | — | 77% | 76% | — | 76% | 68% | 48% | — | 76% |
| 6. | CYP1A1 | 205749_at | 11 | 90% | 82% | 20% | 65% | 73% | 11% | 72% | 74% | 43% | 77% | 73% |
| 7. | CYP1B1 | 202437_s_at | 9 | 88% | 80% | 32% | 65% | 64% | 35% | 64% | 58% | — | — | 65% |
| 8. | PRDM11 | 229687_s_at | 1 | — | — | 50% | — | — | — | — | — | — | — | — |
| 9. | CBR3 | 205379_at | 1 | — | — | — | — | — | 14% | — | — | — | — | — |
| 10. | AKR1C1 | 217626_at | 1 | — | — | — | — | — | 10% | — | — | — | — | — |
| 11. | AKR1C3 | 209160_at | 1 | — | — | — | — | — | 5% | — | — | — | — | — |
| 12. | GRM1 | 207299_s_at | 1 | — | — | — | — | — | 4% | — | — | — | — | — |
| 13. | CYP4Z1 | 237395_at | 1 | — | — | — | — | — | — | — | 67% | — | — | — |
| 14. | UCHL1 | 201387_s_at | 1 | — | — | — | — | — | — | — | 57% | — | — | — |
| 15. | CABYR | 219928_s_at | 1 | — | — | — | — | — | — | — | 54% | — | — | — |
| 16. | GPRC5A | 203108_at | 2 | 100% | 100% | — | — | — | — | — | — | — | — | — |
| 17. | CCDC37 | 243758_at | 1 | — | — | 50% | — | — | — | — | — | — | — | — |
| 18. | GLI3 | 227376_at | 3 | — | — | 38% | — | — | 12% | — | — | 43% | — | — |
| 19. | ABCC3 | 208161_s_at | 3 | — | — | 30% | — | — | — | — | 58% | 52% | — | — |
| 20. | SAMD5 | 228653_at | 3 | — | — | 24% | — | — | 41% | — | 57% | — | — | — |
| 21. | RASSF10 | 238755_at | 5 | — | — | 23% | — | 75% | — | 75% | 68% | 64% | — | — |
| 22. | USP27X | 230620_at | 11 | 99% | 94% | 31% | 100% | 100% | 100% | 100% | 100% | 49% | 100% | 100% |
| 23. | HTR2B | 206638_at | 1 | — | — | — | — | — | 5% | — | — | — | — | — |
| 24. | NR0B1 | 206645_s_at | 5 | — | — | 33% | — | 66% | — | 66% | — | 58% | — | 66% |
| 25. | PLAG1 | 205372_at | 5 | — | — | 26% | 61% | 61% | — | 61% | — | — | — | 61% |
| 26. | SCGB3A1 | 230378_at | 5 | — | — | — | 65% | 58% | — | 58% | 65% | — | — | 58% |
| 27. | LHX6 | 219884_at | 1 | — | — | — | 55% | — | — | — | — | — | — | — |
| 28. | LINC00942 | 1558308_at | 1 | — | — | — | — | — | — | — | — | 52% | — | — |
| 29. | REEP1 | 204364_s_at | 1 | — | — | — | — | — | — | — | — | 45% | — | — |
| 30. | C6orf164 | 230506_at | 1 | — | — | — | — | — | 44% | — | — | — | — | — |
| 31. | LINC00589 | 232718_at | 1 | — | — | — | — | — | 13% | — | — | — | — | — |
| 32. | JAKMIP3 | 233076_at | 4 | — | — | 100% | — | — | 64% | — | 98% | 56% | — | — |
| 33. | LINC00930 | 1556768_at | 3 | — | — | 78% | — | — | 4% | — | — | 100% | — | — |
| 34. | DNHD1 | 229631_at | 1 | — | — | 53% | — | — | — | — | — | — | — | — |
| 35. | TMCC3 | 235146_at | 7 | — | — | 52% | — | 82% | 87% | 82% | 64% | 73% | 84% | — |
| 36. | ADH7 | 210505_at | 3 | — | — | 27% | — | — | 27% | — | — | 54% | — | — |
| 37. | PRKAR2B | 203680_at | 7 | 96% | 96% | — | 76% | 74% | — | 73% | 76% | — | — | 74% |
| 38. | GAD1 | 205278_at | 9 | — | — | 23% | 74% | 67% | 48% | 67% | 73% | 46% | 84% | 67% |
| 39. | LOC338667 | 1564786_at | 3 | — | — | — | — | 65% | — | 65% | — | 43% | — | — |
| 40. | CYB5A | 217021_at | 6 | — | — | — | 65% | 63% | 3% | 63% | 87% | — | — | 64% |
| 41. | PIEZO2 | 219602_s_at | 6 | — | — | 56% | 65% | 60% | — | 60% | — | 68% | — | 60% |
| 42. | SLITRK6 | 235976_at | 4 | — | — | — | 58% | 57% | — | 57% | — | — | — | 57% |
| 43. | KCNA1 | 230849_at | 3 | — | — | — | — | 52% | — | 53% | — | — | — | 53% |
| 44. | LOC100507560 | 231379_at | 9 | — | — | 38% | 48% | 74% | 82% | 74% | 62% | 41% | 100% | 50% |
| AUC% Sensitivity (SD) Specificity (SD) Misclassification Error Rate (SD) |
79% | 74% | 82% | 76.6% | 61.6% | 76% | 77% | 80% | 70% | 57% | 74.7% | |||
| 0.83 (0.14) | 0.81 (0.16) | 0.85 (0.13) | 1 | 0.92 (0.10) | 0.98 (0.04) | 0.84 (0.12) | 0.95 (0.08) | 0.68 (0.17) | 0.69 (0.20) | 0.81 (0.14) | ||||
| 0.5 (0.30) | 0.37 (0.10) | 0.51 (0.29) | 0 | 0.15 (0.13) | 0.02 (0.07) | 0.49 (0.26) | 0.07 (0.15) | 0.66 (0.24) | 0.43 (0.24) | 0.39 (0.14) | ||||
| 0.27 (0.14) | 0.31 (0.15) | 0.25 (0.10) | 0.30 (0.03) | 0.31 (0.06) | 0.30 (0.05) | 0.26 (0.09) | 0.31 (0.09) | 0.32 (0.13) | 0.39 (0.12) | 0.31 (0.11) | ||||
Important index (value) for each gene in any method was reported. The third column indicated number of studies that it confirmed the association of each gene with progression of the COPD. Third column indicated sum of number of methods that it confirmed each gene (Range score: 0 to 11).