Table 1.
ALS dataset analysis
| Transcript quantification | Feature type | Filter | Machine learning Alg. | AUC | Confidence Int. | Sens. | Spec. | Mean features* |
|---|---|---|---|---|---|---|---|---|
| Cufflinks | Genes | None | Elastic Net | 0.496 | 0.283–0.709 | 0.625 | 0.625 | 516 |
| Cufflinks | Genes | None | Random Forest | 0.766 | 0.558–0.973 | 1.000 | 0.750 | 516 |
| Cufflinks | Genes | None | SPLS | 0.606 | 0.391–0.820 | 0.688 | 0.688 | 516 |
| Cufflinks | Genes | MVP | Elastic Net | 0.918 | 0.809–1.000 | 1.000 | 0.813 | 38 |
| Cufflinks | Genes | MVP | Random Forest | 0.883 | 0.756–1.000 | 1.000 | 0.750 | 38 |
| Cufflinks | Genes | MVP | SPLS | 0.863 | 0.719–1.000 | 0.750 | 1.000 | 38 |
| Cufflinks | Isoform Count | None | Elastic Net | 0.781 | 0.601–0.962 | 0.875 | 0.813 | 1146 |
| Cufflinks | Isoform Count | None | Random Forest | 0.815 | 0.643–0.986 | 1.000 | 0.750 | 1146 |
| Cufflinks | Isoform Count | None | SPLS | 0.656 | 0.449–0.863 | 0.698 | 0.813 | 1146 |
| Cufflinks | Isoform Count | MVP | Elastic Net | 0.793 | 0.607–0.979 | 0.813 | 0.813 | 50 |
| Cufflinks | Isoform Count | MVP | Random Forest | 0.879 | 0.752–1.000 | 1.000 | 0.750 | 50 |
| Cufflinks | Isoform Count | MVP | SPLS | 0.715 | 0.516–0.913 | 0.750 | 0.813 | 50 |
| Cufflinks | Isoform Fraction | None | Elastic Net | 1.000 | 1.000–1.000 | 1.000 | 1.000 | 93 |
| Cufflinks | Isoform Fraction | None | Random Forest | 0.840 | 0.687–0.993 | 1.000 | 0.750 | 93 |
| Cufflinks | Isoform Fraction | None | SPLS | 0.938 | 0.815–1.000 | 0.938 | 1.000 | 93 |
| Cufflinks | Isoform Fraction | MVP | Elastic Net | 0.891 | 0.776–1.000 | 1.000 | 0.750 | 47 |
| Cufflinks | Isoform Fraction | MVP | Random Forest | 0.871 | 0.739–1.000 | 1.000 | 0.750 | 47 |
| Cufflinks | Isoform Fraction | MVP | SPLS | 0.938 | 0.815–1.000 | 0.938 | 1.000 | 47 |
| RSEM | Genes | None | Elastic Net | 0.699 | 0.489–0.909 | 0.750 | 0.875 | 631 |
| RSEM | Genes | None | Random Forest | 0.758 | 0.545–0.971 | 1.000 | 0.750 | 631 |
| RSEM | Genes | None | SPLS | 0.746 | 0.561–0.932 | 0.750 | 0.750 | 631 |
| RSEM | Genes | MVP | Elastic Net | 0.824 | 0.653–0.995 | 0.938 | 0.750 | 50 |
| RSEM | Genes | MVP | Random Forest | 0.947 | 0.880–1.000 | 1.000 | 0.750 | 50 |
| RSEM | Genes | MVP | SPLS | 0.500 | 0.265–0.735 | 0.438 | 0.938 | 50 |
| RSEM | Isoform Count | None | Elastic Net | 0.699 | 0.501–0.898 | 0.875 | 0.688 | 740 |
| RSEM | Isoform Count | None | Random Forest | 0.773 | 0.572–0.975 | 1.000 | 0.750 | 740 |
| RSEM | Isoform Count | None | SPLS | 0.746 | 0.566–0.926 | 0.813 | 0.750 | 740 |
| RSEM | Isoform Count | MVP | Elastic Net | 0.910 | 0.811–1.000 | 1.000 | 0.750 | 50 |
| RSEM | Isoform Count | MVP | Random Forest | 0.963 | 0.904–1.000 | 1.000 | 0.875 | 50 |
| RSEM | Isoform Count | MVP | SPLS | 0.672 | 0.451–0.892 | 0.625 | 0.938 | 50 |
| RSEM | Isoform Fraction | None | Elastic Net | 0.664 | 0.463–0.866 | 0.875 | 0.563 | 180 |
| RSEM | Isoform Fraction | None | Random Forest | 0.779 | 0.582–0.977 | 1.000 | 0.750 | 180 |
| RSEM | Isoform Fraction | None | SPLS | 0.816 | 0.643–0.990 | 0.875 | 0.813 | 180 |
| RSEM | Isoform Fraction | MVP | Elastic Net | 0.781 | 0.585–0.978 | 1.000 | 0.750 | 41 |
| RSEM | Isoform Fraction | MVP | Random Forest | 0.902 | 0.787–1.000 | 1.000 | 0.750 | 41 |
| RSEM | Isoform Fraction | MVP | SPLS | 0.949 | 0.871–1.000 | 1.000 | 0.875 | 41 |
| SeqGSEA | Genes | None | Elastic Net | 0.637 | 0.435–0.839 | 0.813 | 0.563 | 331 |
| SeqGSEA | Genes | None | Random Forest | 0.770 | 0.565–0.974 | 1.000 | 0.75 | 331 |
| SeqGSEA | Genes | None | SPLS | 0.820 | 0.666–0.975 | 0.813 | 0.750 | 331 |
| SeqGSEA | Genes | MVP | Elastic Net | 0.785 | 0.608–0.963 | 0.813 | 0.750 | 47 |
| SeqGSEA | Genes | MVP | Random Forest | 0.981 | 0.946–1.000 | 0.938 | 0.938 | 47 |
| SeqGSEA | Genes | MVP | SPLS | 0.750 | 0.553–0.947 | 0.813 | 0.750 | 47 |
| SeqGSEA | Exon Count | None | Elastic Net | 0.473 | 0.259–0.687 | 0.438 | 0.750 | 1181 |
| SeqGSEA | Exon Count | None | Random Forest | 0.770 | 0.565–0.974 | 1.000 | 0.750 | 1181 |
| SeqGSEA | Exon Count | None | SPLS | 0.820 | 0.647–0.994 | 0.688 | 1.000 | 1181 |
| SeqGSEA | Exon Count | MVP | Elastic Net | 0.906 | 0.781–1.000 | 0.938 | 0.875 | 50 |
| SeqGSEA | Exon Count | MVP | Random Forest | 0.996 | 0.985–1.000 | 1.000 | 0.938 | 50 |
| SeqGSEA | Exon Count | MVP | SPLS | 0.934 | 0.818–1.000 | 0.875 | 1.000 | 50 |
| SeqGSEA | Exon Fraction | None | Elastic Net | 0.844 | 0.701–0.986 | 0.813 | 0.813 | 2669 |
| SeqGSEA | Exon Fraction | None | Random Forest | 0.758 | 0.545–0.971 | 1.000 | 0.750 | 2669 |
| SeqGSEA | Exon Fraction | None | SPLS | 0.766 | 0.558–0.973 | 1.000 | 0.750 | 2669 |
| SeqGSEA | Exon Fraction | MVP | Elastic Net | 0.672 | 0.466–0.878 | 0.750 | 0.750 | 50 |
| SeqGSEA | Exon Fraction | MVP | Random Forest | 0.797 | 0.612–0.982 | 1.000 | 0.750 | 50 |
| SeqGSEA | Exon Fraction | MVP | SPLS | 0.785 | 0.590–0.980 | 1.000 | 0.750 | 50 |
*Mean number of transcripts selected as features per leave-two-out cross-validation test.