Table 1.
List of mutational and CNA features for cancer driver genes
| Attribute name | Description |
|---|---|
| CNA_cbs_countGain | # samples in cohort with CBS value > 1.1 |
| CNA_cbs_countLoss | # samples in cohort with CBS value < 1.1 |
| CNA_cbs_logratio_GvL | Log10-ratio of countGain VS countLoss |
| CNA_gain_freq | # samples in cohort with CBS value > 1.1 / cohort size |
| CNA_loss_freq | # samples in cohort with CBS value < 1.1 / cohort size |
| MUTS_clusters_miss_VS_pam | Log10-ratio of missense VS PAM within OncodriveCLUST peaks |
| MUTS_freq_clustered | # of mutations in OncodriveCLUST peaks / # of samples with gene mutated |
| MUTS_freq_disruptive | # of samples with truncating mutations or high impact missense / # of samples having gene mutations |
| MUTS_freq_missH | # of high impact missense mutations not in OncodriveCLUST peaks / # samples with gene mutated |
| MUTS_freq_missHM | # of high and medium impact missense mutations not in OncodriveCLUST peaks / # samples with gene mutated |
| MUTS_freq_truncating | # of samples with truncating mutations / # of samples with at least one mutation |
| MUTS_missense_clustercov | # missense mutations in OncodriveCLUST peaks / # missense mutations / # amino acids covered by peaks |
| MUTS_missense_mutrec | # recurrent missense mutations / # high and medium impact missense mutations |
| MUTS_missense_rec_freq | # recurrent missense mutations / # mutations (as in Vogelstein et al.) |
| MUTS_missense_recHM | # samples with high and medium impact recurrent missense mutations / # samples with missense mutations |
| MUTS_OncoFM_pvalue | OncodriveFM P-value |
| MUTS_pams_count | # samples with PAM |
| MUTS_pams_freq | # samples with PAM / # samples with gene mutations |
| MUTS_pams_ratio | # samples with PAM VS # samples with no PAM |
| MUTS_pamsrec_freq | # samples with PAM VS # of samples with gene mutation |
| MUTS_trunc_count | # samples with truncating mutations |
| MUTS_trunc_freq_cohort | # of truncating mutations / # of samples with gene mutations |
| MUTS_trunc_mutfreq | # truncating mutations / # mutations (as in Vogelstein et al.) |
| MUTS_trunc_vs_missbenign_ratio | # samples with truncating mutations VS # samples with benign missense mutations |
| MUTS_trunc_vs_missense_ratio | # samples with truncating mutations VS # samples with missense mutations |
| MUTS_trunc_vs_notrunc_ratio | # samples with truncating mutations VS # samples without truncating mutations |
| MUTS_tuson_missHM_missbenign_ratio | # samples with high and medium impact mutations VS # samples with benign missense mutations (as described in Davoli et al.) |
| MUTS_tuson_splicing_missbenign_ratio | # samples splicing variants mutations VS # samples with benign missense mutations (as described in Davoli et al.) |
| MUTS_tuson_trunc_missbenign_ratio | # samples with truncating (excluding splicing variants) mutations VS # samples with benign missense mutations (as described in Davoli et al.) |
Note: List of features initially created for characterizing LoF and Act genes. The description reflects the formula applied for the calculation of the features. All features elaborated describe either mutation or CNA characteristics. Abbreviations used in the descriptions are: # (number sign): Count/number of, / (slash): divided by, CBS : circular binary segmentation, truncating mutations: frameshift, stop gained and lost, splice donor and acceptor, missense: all missense mutations and insertions and deletions not altering the reading frame, high and medium impact mutations: all missense mutations with and TransFIC impact of 1 and 2 , benign missense: all missense with low or unknown TransFIC impact, PAM : protein affecting: frameshift, stop gained and lost, splice donor and acceptor, missense, (gene) mutations: all mutations-affecting coding sequence, VS : versus—a ratio has been obtained.