Evaluation of copy number variation and gene expression in neurofibromatosis type-1-associated malignant peripheral nerve sheath tumours

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
4		0.00106	DAB2	3.46	2.65
5	Cell adhesion: PLAU signalling	0.00445	HGF	7.80	10.97
5	Cell adhesion: PLAU signalling	0.00445	SERPINE1	5.74	4.54
6	Role of alpha-6/beta-4 integrins in carcinoma progression	0.00589	HGF	7.80	10.97
6	Role of alpha-6/beta-4 integrins in carcinoma progression	0.00589	LIMK1	2.04	2.23
7	Development: TGF-beta-dependent induction of EMT via MAPK	0.00641	DAB2	3.46	2.65
7	Development: TGF-beta-dependent induction of EMT via MAPK	0.00641	SERPINE1	5.74	4.54
8	Transport: macropinocytosis regulation by growth factors	0.01130	HGF	7.80	10.97
8	Transport: macropinocytosis regulation by growth factors	0.01130	LIMK1	2.04	2.23
9	Development: regulation of epithelial-to-mesenchymal transition (EMT)	0.01165	HGF	7.80	10.97
9		0.01165	SERPINE1	5.74	4.54
10	Transport: clathrin-coated vesicle cycle	0.01421	PREB	1.45	1.43
10	Transport: clathrin-coated vesicle cycle	0.01421	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.

ISSN: 1479-7364