Skip to main content

Table 2 List of the identified driver mutations ordered by CHASM score.

From: Integrative network-based approach identifies key genetic elements in breast invasive carcinoma

Chrom Occurring gene SNV position CHASM score P-value Ref Alt Amino acids Codons SIFT score PolyPhen score
1 PTPRC 198711494 0.158 6.00E-04 G A E/K Gag/Aag Deleterious (0) probably_damaging (0.999)
8 TNKS 9413850 0.162 6.00E-04 C T S/F tCc/tTc Deleterious (0.01) Unknown (0)
X GRIA3 122319694 0.298 0.0119 C A F/L ttC/ttA Deleterious (0) probably_damaging (0.996)
5 PCDHB14 140604126 0.308 0.0134 C T S/L tCg/tTg Deleterious (0.02) Benign (0.368)
X HUWE1 53644041 0.31 0.0136 C A R/L cGa/cTa Deleterious (0) probably_damaging (1)
17 NFE2L1 46136186 0.326 0.0175 C T S/F tCc/tTc Deleterious (0.01) probably_damaging (0.994)
9 NAIF1 130829249 0.336 0.0204 C G K/N aaG/aaC Deleterious (0) probably_damaging (0.995)
2 KLHL23 170592167 0.354 0.0251 C G R/G Cga/Gga Deleterious (0) probably_damaging (0.999)
12 KCNA1 5021107 0.384 0.0406 C T T/M aCg/aTg Deleterious (0) probably_damaging (0.997)
  1. The CHASM score is defined as the fraction of trees in the Random Forest that voted for the mutation being classified as a passenger. Lower scores increase the confidence of driver mutations. P-values are calculated based on the null score distribution. The table reports also the changes in the related codons and amino acids. The SIFT and PolyPhen scores refer to the prediction of whether an amino acid substitution affects the function and structure of the human proteins. The SIFT prediction is based on the degree of conservation of amino acid residues in sequence alignments derived from closely related sequences (lower scores represent high impacts), whereas the PolyPhen prediction uses physical and evolutionary comparative considerations (higher scores represent high impact and severe influence on the protein function and structure).