Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis

BMC Bioinformatics

Table 1 Enrichment of genes encoding protein kinases, transcription factors, and genes linked to these categories in the global network

	Driver mutations			GO term	No. of genes	No. of network edges, total	No. of shared genes	FDR(GSEA)	No. of network links	FDR(NEA)
Set	Type	No. of genes	No. of network edges, total	Title	No. of genes	No. of network edges, total	No. of shared genes	FDR(GSEA)	No. of network links	FDR(NEA)
GBM	Point mutations	277	40863	Protein kinase activity	277	49534	50	1.10e-63	3680	0.00e + 00
	Point mutations	277	40863	Regulation of transcription, DNA dependent	453	84621	19	1.05e-05	2340	1.14e-40
	Copy number	455	49817	Protein kinase activity	277	49534	32	2.79e-18	3379	0.00e + 00
	Copy number	455	49817	Regulation of transcription, DNA dependent	453	84621	40	2.99e-16	2817	1.87e-44
OV	Point mutations	1611	168022	Protein kinase activity	277	49534	103	1.52e-50	10941	0.00e + 00
	Point mutations	1611	168022	Regulation of transcription, DNA-dependent	453	84621	93	8.99e-19	9766	0.00e + 00
	Copy number	168	24513	Protein kinase activity	277	49534	12	1.71e-07	1247	0.00e + 00
	Copy number	168	24513	Regulation of transcription, DNA-dependent	453	84621	7	0.29	1289	1.15e-11

FDR (GSEA): significance for fractions of PK and TF as shared genes.
FDR (NEA): significance for fractions of genes connected to PK and TF in the network.

ISSN: 1471-2105