Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure

Table 7 Enriched human pathways for susceptibility to breast cancer

KEGG pathway ID	Pathway description	SEPEA_NT3	SEPEA_NT3*
[path:hsa04370]	VEGF signaling pathway	1.69E-04	5.14E-04
[path:hsa04662]	B-cell receptor signaling	3.32E-04	3.51E-04
[path:hsa04630]	Jak-STAT signaling	8.91E-04	0.0417
[path:hsa04520]	Adherens junction	0.0014	0.1438
[path:hsa04810]	Regulation of actin cytoskeleton	0.0027	0.0717
[path:hsa04150]	mTOR signaling	0.0047	0.0052
[path:hsa04664]	Fc epsilon RI signaling	0.0081	5.99E-04
[path:hsa04510]	Focal adhesion	0.0103	0.0648
[path:hsa04012]	ErbB signaling	0.0103	8.51E-04
[path:hsa04210]	Apoptosis	0.0108	7.97E-04
[path:hsa03440]	Homologous recombination	0.0147	0.0016
[path:hsa04660]	T cell receptor signaling	0.0182	0.001
[path:hsa04010]	MAPK signaling	0.0183	0.0183
[path:hsa04910]	Insulin signaling	0.0191	0.0032
[path:hsa04514]	Cell adhesion molecules	0.0274	0.2407
[path:hsa04115]	P53 signaling	0.0306	0.0093
[path:hsa04620]	Toll-like receptor signaling pathway	0.0391	0.0193

Enriched KEGG [44] pathways (with P-value ≤ 0.05) obtained using genes from the OMIM database [49] that confer susceptibility to breast cancer. P-values were obtained using the SEPEA_NT3 and SEPEA_NT3* analysis.

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