Table 2.
Prediction performance (AUC) of different predictors in predicting immunogenic neoantigens
| Predictor | NCI set | Literature set |
|---|---|---|
| tumor_rna_alt_freq | 0.593 | – |
| tumor_rna_depth | 0.586 | – |
| tumor_rna_alt_reads | 0.642 | – |
| TCGA_TPM_subtype_matched | 0.641 | 0.641 |
| TCGA_TPM_pancancer | 0.613 | 0.613 |
| TCGA_TPM_subtype_mismatched | 0.520 | 0.541 |
| IC50 | 0.723 | 0.628 |
| EL_Rank | 0.729 | 0.614 |
| AXEL-F (EL_to_IC50, tumor_rna_alt_reads) | 0.753 | — |
| AXEL-F (EL_to_IC50, TCGA_TPM_pancancer) | 0.735 | 0.632 |
| AXEL-F (EL_to_IC50, TCGA_TPM_subtype_mismatched) | 0.669 | 0.606 |
| AXEL-F (EL_to_IC50, TCGA_TPM_subtype_matched) | 0.754 | 0.646 |
| MHCflurry | 0.779 | 0.639 |
| AXEL-F (MHCflurry, TCGA_TPM_subtype_matched) | 0.799 | 0.659 |
| MixMHCpred | 0.659 | 0.645 |
| HLAthena (TCGA_TPM_subtype_matched) | 0.756 | 0.657 |