Table 1.

Pathways identified in the Italian dataset using linear combination test analysis^a

Rank	Pathway name	Source	Pathway size (genes)	P-value (LCT)	FDR
1	TNF/stress-related signaling pathway	BioCarta	25	0.0007	0.180
2	Bole of MAL in Rho-mediated activation of SRF pathway	BioCarta	19	0.0009	0.180
3	Antigen processing and presentation	KEGG	88	0.0011	0.180
4	Hypoxia and p53 in the cardiovascular system pathway	BioCarta	23	0.0019	0.192
5	Glycerophospholipid metabolism	KEGG	66	0.0022	0.192
6	Chaperones modulate interferon signaling pathway	BioCarta	19	0.0023	0.192
7	Small cell lung cancer	KEGG	87	0.0035	0.218
8	Acetylation and deacetylation of RelA in the nucleus pathway	BioCarta	16	0.0047	0.245
9	Signal transduction through IL1R pathway	BioCarta	33	0.0059	0.269
10	CBL-mediated ligand-induced downregulation of EGF receptors pathway	BioCarta	13	0.0066	0.276
11	Rho cell motility signaling pathway	BioCarta	32	0.0092	0.333
12	Role of PI3K subunit p85 in the regulation of actin organization and cell migration pathway	BioCarta	16	0.0120	0.377
13	Non-small cell lung cancer	KEGG	54	0.0154	0.436
14	Phosphatidylinositol signaling system	KEGG	77	0.0156	0.436
15	VEGF signaling pathway	KEGG	74	0.0232	0.582
16	Calcium signaling pathway	KEGG	179	0.0282	0.582
17	CD40L signaling pathway	BioCarta	15	0.0300	0.582
18	Endometrial cancer	KEGG	52	0.0311	0582
19	Cyclins and cell Cycle regulation pathway	BioCarta	23	0.0313	0.582
20	MAPK signaling pathway	KEGG	267	0.0335	0.582
21	Complement and coagulation cascades	KEGG	69	0.0383	0.636
22	Hedgehog signaling pathway	KEGG	57	0.0438	0.636
23	Graft-versus-host disease	KEGG	42	0.0460	0.636
24	Ras-independent pathway in NK cell-mediated cytotoxicity pathway	BioCarta	20	0.0469	0.636
25	Classical complement pathway	BioCarta	14	0.0484	0.639

Abbreviations: FDR, false discovery rate; KEGG, Kyoto Encyclopedia of Genes and Genomes; LCT, linear combination test.

^aAll pathways with P < 0.05 are shown.