Table 4.
P values (Wilcoxon rank-sum test) for somatic mutations (recurrent vs. non-recurrent) in the COSMIC database. Comparisons are done for variants in different functional categories. n-rec is the number of recurrent somatic mutations, and n-nonrec is the number of nonrecurrent somatic mutations. The best performing individual functional annotation is also reported.
| Variant Class | n-rec | n-nonrec | Eigen | Eigen-PC | CADD-score v1.0 | CADD-score v1.1 | Best Individual Annotation |
|---|---|---|---|---|---|---|---|
| Regulatory | 21,279 | 428,398 | 2.02E-165 | 5.13E-264 | 1.05E-71 | 2.70E-50 | ≤2.22E-308 (PolIIpval) |
| Intronic | 85,502 | 2,093,158 | 2.40E-155 | 2.13E-112 | 2.89E-61 | 1.09E-10 | ≤2.22E-308 (GERP NR) |
| Downstream | 15,956 | 318,967 | 2.73E-92 | 3.04E-128 | 4.31E-36 | 1.83E-28 | 1.01E-155 (GERP NR) |
| Upstream | 14,636 | 309,615 | 1.28E-52 | 2.01E-84 | 7.90E-24 | 3.21E-17 | 9.68E-86 (PolIIPval) |
| Noncoding Change | 4,903 | 66,717 | 2.51E-07 | 2.49E-21 | 1.51E-01 | 4.84E-05 | 8.13E-35 (PolIIPval) |
| 3′UTR | 2,236 | 28,261 | 6.94E-03 | 4.22E-04 | 1.06E-05 | 3.37E-01 | 5.67E-05 (GERP NR) |
| 5′UTR | 417 | 3,908 | 1.14E-02 | 2.32E-01 | 6.43E-02 | 1.15E-01 | 2.79E-07 (GERP NR) |
| Intergenic | 75,327 | 2,182,466 | 1.49E-02 | 3.97E-06 | 1.08E-06 | 6.30E-16 | 1.19E-18 (H3K4Me1) |
| Synonymous | 434 | 2,388 | 1.09E-01 | 9.69E-01 | 8.25E-01 | 2.88E-01 | 2.16E-03 (PhyloPri) |