Table 4.

Indications of the p-values for comparison of mutation occurrences, in the oncoprotein, tumor suppressor protein and total coding region sets, for the STAD dataset, when silent mutations are either included or removed. (These data are compiled from the SOM files labeled, “SOM STAD, new tumor_results” and “SOM STAD, neg and pos outcome_results.”) In all cases, the p-values represent higher numbers of mutations in the no-subsequent tumor group and in the positive outcome group. The new tumor group represents 74 barcodes and the no-subsequent tumor group represents 224 barcodes. The negative outcome group represents 32 barcodes and the positive outcome group represents 71 barcodes.

	Oncoprotein		Tumor Suppressor		Total
	New Tumor vs No-subsequent tumor	Neg vs Pos Outcome	New Tumor vs No-subsequent tumor	Neg vs Pos Outcome	New Tumor vs No-subsequent tumor	Neg vs Pos Outcome
Silent Included	0.007	0.041	0.018	0.072	0.004	0.129
Silent Removed	0.017	0.036	0.026	0.104	0.004	0.128