Table 1 Description of 12 predictive genome features
Genome features | Explaination and note | Source |
|---|---|---|
Expression level | Average expression level across 91 cell lines in the CCLE [38] | MutSigCV[7] |
DNA replication time | Scale of 100 (early) to 1500 (late) | MutSigCV [7] |
HiC-derived metric | The chromosomal compartment localization of the gene | MutSigCV [7] |
Length of genomic regions | Combined coding regions | WITER [39] |
Constraint score for non-synonymous mutations | Normalized student residues | Samocha et al. [40] |
Expression hubs | Hubness in a gene expression network | MERGE [41] |
Known regulators | Gene’s known regulatory role based on gene annotation databases | MERGE [41] |
Genomic CNV | Genomic CNV status | MERGE [41] |
Methylation | Methylation status | MERGE [41] |
Total mutation number among patients | Calculation based on local MAF | – |
Harmful mutation number among patients (null and nonsilent effects) | Calculation based on local MAF | – |
Standard deviation of FISs across patients | Calculation based on local MAF | – |