Table 2.
A summary of the associations we found with elevated somatic mutation burden in individual gene sets in individual cancers
| Gene set | Cancer | Patients with PGV | Additional clonal nonsynonymous mutations per MB | p value | Adjusted p value |
|---|---|---|---|---|---|
| TP53 regulates transcription of DNA repair genes | UCEC | 14 | 38.78 | 8.712E-31 | 2.004E-29 |
| DNA repair | UCEC | 31 | 25.71 | 7.358E-30 | 8.462E-29 |
| Transcriptional regulation by TP53 | UCEC | 20 | 27.86 | 4.704E-23 | 3.607E-22 |
| Generic transcription pathway | UCEC | 22 | 26.34 | 1.132E-22 | 6.508E-22 |
| Disease | UCEC | 12 | 34.18 | 5.317E-21 | 2.446E-20 |
| Gene expression transcription | UCEC | 24 | 23.87 | 1.828E-20 | 7.009E-20 |
| Mismatch repair, diseases of mismatch repair (MMR) | UCEC | 7 | 34.55 | 3.925E-13 | 1.290E-12 |
| Sumoylation | UCEC | 6 | 31.43 | 9.928E-10 | 2.854E-09 |
| Deubiquitination | UCEC | 6 | 31.15 | 1.396E-09 | 3.568E-09 |
| Fanconi anemia pathway | UCEC | 8 | 25.54 | 1.040E-08 | 2.393E-08 |
| DNA double-strand break response | UCEC | 7 | 26.42 | 2.932E-08 | 6.130E-08 |
| G2 M checkpoints, G2 M DNA damage checkpoint, regulation of TP53 activity, regulation of TP53 activity through phosphorylation | UCEC | 9 | 20.00 | 1.958E-06 | 3.753E-06 |
| Post-translational protein modification | UCEC | 9 | 19.61 | 3.065E-06 | 5.423E-06 |
| Cell cycle checkpoints | UCEC | 10 | 17.62 | 9.955E-06 | 1.635E-05 |
| Disease | COAD | 8 | 20.53 | 4.064E-06 | 7.315E-05 |
| DNA double-strand break repair | UCEC | 15 | 11.48 | 4.291E-04 | 6.580E-04 |
| Cell cycle | UCEC | 15 | 11.37 | 4.835E-04 | 6.950E-04 |
| DNA repair | SKCM | 30 | 7.89 | 6.214E-04 | 1.243E-02 |
| Disease | SKCM | 6 | 16.17 | 1.680E-03 | 1.680E-02 |
| Cell cycle | SKCM | 20 | 8.43 | 2.805E-03 | 1.870E-02 |
| Generic transcription pathway, gene expression transcription | COAD | 15 | 9.86 | 2.467E-03 | 2.220E-02 |
| Cell cycle checkpoints | SKCM | 12 | 9.57 | 8.553E-03 | 2.851E-02 |
| Regulation of TP53 activity | SKCM | 11 | 10.38 | 6.340E-03 | 2.851E-02 |
| DNA double-strand break repair | SKCM | 19 | 7.72 | 7.643E-03 | 2.851E-02 |
| Homology-directed repair (HDR) through homologous recombination (HRR) | SKCM | 17 | 7.85 | 1.027E-02 | 2.903E-02 |
| Resolution of D-loop structures, resolution of D-loop structures through synthesis-dependent strand annealing (SDSA), homologous DNA pairing, and strand exchange | SKCM | 16 | 7.96 | 1.161E-02 | 2.903E-02 |
| Generic transcription pathway, gene expression transcription | SKCM | 18 | 6.90 | 2.029E-02 | 3.568E-02 |
| G2 M checkpoints, G2 M DNA damage checkpoint, regulation of TP53 activity through phosphorylation | SKCM | 10 | 9.52 | 1.696E-02 | 3.568E-02 |
| Transcriptional regulation by TP53 | SKCM | 16 | 7.44 | 1.827E-02 | 3.568E-02 |