MSigDB category
|
Gene set name
|
Somatic variant caller
|
Gene
|
P-value
|
RAREVATOR P-value
|
|---|
BP | SYSTEM PROCESS | VarScan | CLCN1 | 0.0054 | 0.0051 |
CM | MODULE 46 | VarScan | CR1 | 0.0009 | 0.0009 |
CM | MODULE 75 | VarScan | CR1 | 0.0032 | 0.0031 |
REACTOME | IMMUNE SYSTEM | muTect | CR1 | 0.0103 | 0.0099 |
- Significantly mutated pathways identified by DrGaP algorithm by using the somatic mutations detected by MuTect and VarScan2 on the uveal melanoma dataset. The table reports the p-value calculated by DrGaP on MuTect and VarScan2 mutations, with and without the RRA variants. Columns report the MSigDB gene set category, the gene set name, the algorithm used for calling somatic variants, the RRA gene that belong to gene set, the DrGaP p-values calculated on the somatic variants (p-value) before and after the addition of the RRA variants detected by RAREVATOR (RAREVATOR P-value).
