Table 3. P values of the selective sixteen out of eighty-nine pathways and gene sets with enrichment of genes with copy number gains (the complete eighty-nine gene sets are listed in Table S3).

	MSigDB ID of gene set: brief description	Blood	Non-involved lung	Discovery set	Validation set	Early stage tumors	Late stage tumors	All tumors
1	AGUIRRE_PANCREAS_CHR8: Genes on chromosome 8 with copy-number-driven expression in pancreatic adenocarcinoma.	0.46	<5×10−5	<5×10−5	<5×10−5	<5×10−5	5×10−5	<5×10−5
2	BRCA_PROGNOSIS_NEG: Genes whose expression is consistently negatively correlated with breast cancer outcomes - higher expression is associated with metastasis and poor prognosis	0.64	<5×10−5	<5×10−5	<5×10−5	<5×10−5	<5×10−5	<5×10−5
3	SMITH_HCV_INDUCED_HCC_UP: Genes highly expressed in hepatitis C-related hepatocellular carcinoma	0.57	<5×10−5	0.00025	5×10−5	<5×10−5	0.00085	5×10−5
4	HSA04514_CELL_ADHESION_MOLECULES: Genes involved in cell adhesion molecules (CAMs)	0.029	0.39	0.00085	0.00040	0.0049	0.00025	0.00040
5	ONCOGENE: Census of human cancer genes	0.37	0.51	0.0011	0.0047	0.0018	0.015	0.00065
6	G_PROTEIN_SIGNALING: Genes involved in G protein signaling	0.41	<5×10−5	0.0016	0.0021	0.0030	0.011	0.0010
7	HSA04610_COMPLEMENT_AND_COAGULATION_CASCADES: Genes involved in complement and coagulation cascades	0.14	<5×10−5	0.0012	0.0028	0.00065	0.0036	0.00145
8	CELL_ADHESION: The attachment of a cell, either to another cell or to the extracellular matrix, via cell adhesion molecules.	0.00050	0.76	0.0026	0.0041	0.012	0.0012	0.0024
9	AT1RPATHWAY: Binding of angiotensin II to AT1-R activates Ca2+ signaling and the JNK pathway.	0.00050	<5×10−5	0.0041	0.0038	0.0068	0.016	0.0031
10	AGUIRRE_PANCREAS_CHR7: Genes on chromosome 7 with copy-number-driven expression in pancreatic adenocarcinoma.	0.93	<5×10−5	0.018	0.00025	0.0026	0.0019	0.0033
11	EDG1PATHWAY: The lipid S1P is an EDG1 ligand promoting chemotaxis via Rac1 and cell survival and proliferation via ERK activation.	0.031	<5×10−5	0.015	0.0089	0.010	0.022	0.0085
12	LOTEM_LEUKEMIA_UP: Genes upregulated in myeloid leukemia and normally expressed in other bodily tissues.	0.62	<5×10−5	0.0048	0.033	0.0077	0.041	0.0089
13	BRCA_ER_NEG: Genes whose expression is consistently negatively correlated with estrogen receptor status in breast cancer - higher expression is associated with ER-negative tumors	0.84	0.94	0.0069	0.0099	0.0037	0.012	0.0090
14	MCALPAINPATHWAY: In integrin-mediated cell migration, calpains digest links between the actin cytoskeleton and focal adhesion proteins.	0.80	<5×10−5	0.019	0.0080	0.0078	0.047	0.010
15	HSA05211_RENAL_CELL_CARCINOMA: Genes involved in renal cell carcinoma	0.32	0.32	0.023	0.031	0.0082	0.025	0.020
16	WNT_SIGNALING: Wnt signaling genes	0.17	0.31	0.020	0.025	0.021	0.0077	0.024