Table 1. The definition of pathways.

Positive Effects
TP53	PIK3C1/AKT	PI3KC2	RAS	RB
CDKN2A	AKT1	PIK3C2A	ARAF	CDKN1A
TTP53	AKT2	PIK3C2B	BRAF	CDKN1B
	AKT3	PIK3C2G	EGFR	CDKN2A
	GAB1		ERBB2	CDKN2B
	IRS1		ERBB3	CDKN2C
	PIK3CA		FGFR1	RB1
	PIK3CB		FGFR2
	PIK3CD		GRB2
	PIK3CG		HRAS
	PIK3CR1		IGFR
	PIK3CR2		KRAS
	PDPK1		MET
	SRC		NRAS
			PDGFRA
			PDGFRB
			RAF1

We split all genes into those with negative effects on the pathway and those with positive effects. Each column is headed by the name of the signaling pathway in which the genes reside, followed by the list of genes. A gene with positive effect increases the generation of the pathway's product when amplified, while a negative effect gene decreases its production when amplified. Deletion of a gene has the reverse effect on the pathway.