Table 3.

Pathway Enrichment analysis

	Pathway name	P value	Genes	Fold change (3 benign vs. 3 malignant)	Fold change (4 benign vs. 5 malignant
1	Glutathione metabolism	0.00056	GSTM1	−3.25	−2.27
			GSTM2	−3.25	−2.27
			GSTM4	−3.25	−2.27
2	Glutathione metabolism/human version	0.00059	GSTM1	−3.25	−2.27
			GSTM2	−3.25	−2.27
			GSTM4	−3.25	−2.27
3	Glutathione metabolism/rodent version	0.00073	GSTM1	−3.25	−2.27
			GSTM2	−3.25	−2.27
			GSTM4	−3.25	−2.27
4	Development: Wnt signalling pathway. Degradation of beta-catenin in the absence Wnt signalling	0.00106	CSNK1D	2.42	1.99
			DAB2	3.46	2.65
5	Cell adhesion: PLAU signalling	0.00445	HGF	7.80	10.97
			SERPINE1	5.74	4.54
6	Role of alpha-6/beta-4 integrins in carcinoma progression	0.00589	HGF	7.80	10.97
			LIMK1	2.04	2.23
7	Development: TGF-beta-dependent induction of EMT via MAPK	0.00641	DAB2	3.46	2.65
			SERPINE1	5.74	4.54
8	Transport: macropinocytosis regulation by growth factors	0.01130	HGF	7.80	10.97
			LIMK1	2.04	2.23
9	Development: regulation of epithelial-to-mesenchymal transition (EMT)	0.01165	HGF	7.80	10.97
			SERPINE1	5.74	4.54
10	Transport: clathrin-coated vesicle cycle	0.01421	PREB	1.45	1.43
			DAB2	3.46	2.65

The pathways were ranked by hypergeometric P values, and a summary of the top ten pathways is reported. The P value represents the probability that a gene set of this size would co-occur by chance alone. Network objects represent the ratio of the number of genes from the list compared to the total number of genes known to be associated with the pathway.