Table 5 Gene characteristics associated with the number of missense, nonsense and frameshift mutations analyzed together in 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 silent mutations in the gene | 265.2 | 3.6x− 1328 | 0.90 |
Gene size in nucleotides | 172.5 | 2.7x− 856 | 0.81 |
“reptime” from MutsigCV | 28.0 | 2.1x− 128 | 0.23 |
Relative replication time | −26.8 | 6.5x− 120 | − 0.21 |
Gene expression in CCLE cancer cell lines* | −24.8 | 1.2x− 106 | − 0.19 |
“hic” from MutsigCV | −23.8 | 8.0x− 100 | − 0.19 |
Percentage of “CpG” | −17.9 | 1.8x− 62 | − 0.14 |
Percentage of “G” | − 17.7 | 1.8x− 61 | − 0.14 |
“expr” from MutsigCV | −17.0 | 3.1x−57 | − 0.14 |
Percentage of “A” | 15.3 | 7.3x− 48 | 0.12 |
Nucleotide diversity | 14.4 | 4.9x− 43 | 0.11 |
Percentage of “C” | −9.0 | 5.6x−19 | − 0.07 |
Percentage of “T” | 8.0 | 1.6x− 15 | 0.06 |
Chromatin accessibility | − 7.5 | 1.0x− 13 | − 0.06 |
Density of SNPs (1 K Genomes Project) | −4.7 | 1.6x− 6 | −0.04 |
Evolutionary conservation | 2.4 | 8.4x−3 | 0.02 |