Table 3 Gene characteristics associated with the number of nonsense mutations in the univariate linear regression model
From: Gene characteristics predicting missense, nonsense and frameshift mutations in tumor samples
Predictor | T-test | P-value | Beta (ß) | |
|---|---|---|---|---|
Number of potential nonsense mutation sites | 91.3 | 3.1 × 10− 427 | 0.59 | |
Gene size in nucleotides | 84.7 | 7.8 × 10− 395 | 0.56 | |
Number of silent mutations in the gene | 80.0 | 1.6 × 10−371 | 0.54 | |
Percentage of “A” | 24.2 | 1.4 × 10−102 | 0.19 | |
Percentage of “G” | −22.6 | 1.0 × 10−91 | −0.18 | |
Percentage of “CpG” | − 21.9 | 1.2 × 10−87 | 0.01 | |
“reptime” from MutsigCV | 20.1 | 2.6 × 10−76 | 0.17 | |
Percentage of “C” | −19.6 | 1.0 × 10− 72 | − 0.15 | |
Relative replication time | − 19.4 | 1.7 × 10− 71 | − 0.15 | |
“hic” from MutsigCV | − 17.1 | 4.5 × 10−58 | − 0.14 | |
“expr” from MutsigCV | −16.0 | 1.1 × 10− 51 | − 0.13 | |
Percentage of “T” | 14.4 | 2.7 × 10− 43 | 0.11 | |
Nucleotide diversity | 12.6 | 2.0 × 10− 34 | 0.10 | |
Gene expression in CCLE cancer cell lines* | −11.2 | 1.1 × 10− 27 | − 0.09 | |
Density of SNPs (1 K Genomes Project) | −8.8 | 3.5 × 10−18 | −0.07 | |
Evolutionary conservation | 5.0 | 3.7 × 10−7 | 0.04 | |
Chromatin accessibility | −4.9 | 6.7 × 10− 7 | −0.04 |