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

BMC Genomics

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

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)

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).

ISSN: 1471-2164