Table 1.
Feature overview.
| Feature (abbreviation) | Description | p-Value |
|---|---|---|
| SelfSim | Self-similarity (mutant vs. normal peptide) (23) | p = 0.24 |
| DAI | Differential agretopicity index (11) | p = 0.96 |
| Mutation position | Position in peptide with mutation. | 10-mer gap p= 0.01, prop test |
| Mutation consequence | The course of mutation | p = NS, prop test |
| CelPrev | Cellular prevalence (24) | p =0.016 |
| Expression | Expression level (25) | p =0.16 |
| VarAlFreq | Variant allele frequency (8, 26) | p =0.72 |
| ValMutRNACoef | Validation of mutation in RNA sequencing | p = NS. (prop test and wilcox test) |
| Foreigness | Foreignness score (27, 28) | p = 0.24 |
| PrioScore | Priority score (8) | p = 0.088 |
| RankBA | Peptide–MHC binding with binding affinity % Rank (22) | p = 8.9·10−9 |
| RankEL | Peptide–MHC binding with eluted ligand % Rank (22) | p = 0.0038 |
| Stability | Peptide–MHC stability (29) | p = 0.012 |
| NetMHCExp | NetMHCpanExp (30) | p = 0.15 |
| PropHydroAro | Proportion of hydrophobic and aromatic residues (31) | p = < 2.22·10−16 |
| Prime | PRIME score (32) | p = 9.3·10−13 |
| HydroCore | Mean hydrophobicity in core (without anchor residues) (33) | p = 1.6·10−12 |
| HydroAll | Mean hydrophobicity entire peptide (33) | p = 3.1·10−12 |
| Aro | Aromaticity (31, 33) | p = 0.029 |
| PropAro | Proportion of aromatic residues in non-anchor positions | p = 2.6·10−09 |
| CysRed | Cysteine residues (31) | p = 1.5·10−05 |
| PropSmall | Proportion of small amino acids in non-anchor positions | p = 0.003 |
| PropAcidic | Proportion of acidic amino acids in in non-anchor positions | p = 0.003 |
| Inst | Peptide instability (31) | p = 0.014 |
| PropBasic | Proportion of basic amino acids in non-anchor positions of peptide | p = 0.088 |
| pI | Isoelectric point (34) | p = 0.120 |
| mw | Molecular weight (31) | p = 0.029 |
Feature abbreviation and a short description of the features. The p-values were all calculated using Wilcoxon test with Bonferroni-adjusted p-value in addition to the p-values specified by prop-test. The color code defines the feature category.
