Table 3. Median scores and feature values for oncogene and tumor suppressor gene hotspot regions.
Thirty genes classified as OGs or TSGs in Landscapes benchmark. The genes contain a total of 114 tumor-type-specific hotspot regions. Each row in the table shows the median Naive Bayes classification score for the regions in the gene. Scores close to 1.0 predict that a region is in an OG and scores close to 0.0 predict that region is in a TSG. Genes are ranked in decreasing order by the Naive Bayes scores. Ranking generally agrees with the Landscapes benchmark. Also shown for each gene is the median value of the six features used to train the Naive Bayes classifier. The features are region size (number of residues), mutational diversity, vertebrate evolutionary conservation (Shannon entropy of alignment position, where lower entropy=higher conservation), mutation net hydrophobicity change, residue solvent accessibility and mutation net volume change.
| Gene | Landscapes Benchmark | Naïve Bayes score | Region Size | Mutational diversity | Conservation | Change in Hydrophobicity | Residue Solvent Accessibility | Change in Volume |
|---|---|---|---|---|---|---|---|---|
| FGFR3 | OG | 1.00 | 1.00 | 0.00 | 0.29 | −3.00 | 0.61 | −1.80 |
| KRAS | OG | 1.00 | 2.50 | 0.58 | 0.26 | 4.49 | 0.73 | −1.90 |
| NRAS | OG | 1.00 | 2.50 | 0.37 | 0.25 | 6.24 | 0.49 | −0.98 |
| BCOR | TSG | 1.00 | 1.00 | 0.00 | 0.32 | −5.40 | 0.55 | 0.84 |
| PIK3R1 | TSG | 1.00 | 1.00 | 0.00 | 0.26 | 4.20 | 0.08 | −0.70 |
| BRAF | OG | 1.00 | 4.00 | 0.25 | 0.25 | 8.70 | 0.42 | −0.07 |
| HRAS | OG | 1.00 | 2.00 | 0.62 | 0.32 | 4.72 | 0.43 | −1.27 |
| PTPN11 | OG | 1.00 | 1.00 | 0.00 | 0.41 | 10.80 | 0.25 | −0.75 |
| FGFR2 | OG | 1.00 | 1.50 | 0.13 | 0.41 | 8.91 | 0.34 | −1.81 |
| PPP2R1A | OG | 0.99 | 3.00 | 0.43 | 0.29 | 4.82 | 0.21 | −1.84 |
| PIK3CA | OG | 0.99 | 2.00 | 0.35 | 0.26 | 0.63 | 0.32 | −0.81 |
| MAP2K1 | OG | 0.97 | 2.00 | 0.71 | 0.25 | −1.02 | 0.29 | −0.49 |
| NFE2L2 | OG | 0.97 | 3.00 | 0.69 | 0.27 | −1.49 | 0.30 | −0.34 |
| SF3B1 | OG | 0.96 | 3.00 | 0.30 | 0.25 | 0.01 | 0.23 | 0.29 |
| ERBB2 | OG | 0.93 | 1.50 | 0.41 | 0.31 | −0.95 | 0.20 | −1.27 |
| RET | OG | 0.92 | 1.00 | 0.00 | 0.26 | 2.20 | 0.10 | 1.56 |
| GNAS | OG | 0.84 | 1.00 | 0.33 | 0.29 | −10.73 | 0.38 | 1.10 |
| CIC | TSG | 0.79 | 6.00 | 0.55 | 0.41 | −8.41 | 0.39 | −0.68 |
| SMAD4 | TSG | 0.69 | 5.00 | 0.92 | 0.30 | −5.15 | 0.16 | −0.34 |
| FBXW7 | TSG | 0.61 | 5.00 | 0.72 | 0.28 | −10.28 | 0.27 | 1.96 |
| PTEN | TSG | 0.61 | 6.00 | 1.00 | 0.26 | −1.33 | 0.07 | 0.80 |
| IDH2 | OG | 0.60 | 1.00 | 0.67 | 0.28 | −7.85 | 0.10 | 0.49 |
| SMARCA4 | TSG | 0.11 | 1.00 | 0.00 | 0.30 | −13.30 | 0.08 | 3.78 |
| NOTCH1 | TSG | 0.08 | 1.00 | 0.00 | 0.55 | −0.80 | 0.17 | 0.79 |
| IDH1 | OG | 0.07 | 1.00 | 0.22 | 0.41 | −9.83 | 0.16 | 1.09 |
| SPOP | OG | 0.06 | 7.00 | 0.73 | 0.25 | 1.37 | 0.09 | 2.46 |
| CDKN2A | TSG | 0.05 | 2.00 | 0.58 | 0.60 | −4.27 | 0.35 | −0.57 |
| VHL | TSG | 0.04 | 8.00 | 0.89 | 0.40 | 0.92 | 0.02 | 0.87 |
| EGFR | OG | 0.01 | 8.00 | 0.53 | 0.34 | −1.01 | 0.30 | −0.76 |
| TP53 | TSG | 0.00 | 30.50 | 0.81 | 0.44 | −4.11 | 0.19 | −0.09 |