A computational model to predict bone metastasis in breast cancer by integrating the dysregulated pathways

Zhou, Xionghui; Liu, Juan

doi:10.1186/1471-2407-14-618

BMC Cancer

Table 2 The dysregulated pathways

From: A computational model to predict bone metastasis in breast cancer by integrating the dysregulated pathways

KEGG pathway	Enrichment p-value	Gene ID	Gene symbol	Cox coefficient	Cox p-value	Stability
Cytokine Cytokine Receptor Interaction	0.029	355	FAS	−0.42	0.0048	0.9925
		1235	CCR6	−0.22	0.023	0.905
		1439	CSF2RB	−0.32	0.0046	0.9875
		2322	FLT3	−0.28	0.015	0.93
		3561	IL2RG	−0.20	0.031	0.8125
		3570	IL6R	−0.37	0.027	0.85
		3575	IL7R	−0.23	0.0044	0.995
		4982	TNFRSF11B	−0.22	0.019	0.9125
		6363	CCL19	−0.11	0.033	0.8025
		6375	XCL1	−0.21	0.013	0.9575
		7042	TGFB2	−0.24	0.016	0.9325
		7422	VEGFA	0.15	0.031	0.83
Chemokine Signaling Pathway	0.041	112	ADCY6	0.34	0.032	0.8225
		1235	CCR6	−0.22	0.023	0.905
		3702	ITK	−0.18	0.023	0.87
		3717	JAK2	−0.48	0.0025	1
		5579	PRKCB1	−0.39	0.021	0.8975
		5613	PRKX	−0.26	0.031	0.815
		5829	PXN	0.34	0.021	0.8725
		6363	CCL19	−0.11	0.033	0.8025
		6375	XCL1	−0.21	0.013	0.9575
Cell Cycle	0.012	894	CCND2	−0.27	0.013	0.96
		1021	CDK6	−0.48	0.010	0.955
		1869	E2F1	0.32	0.0015	1
		1870	E2F2	0.33	0.031	0.8375
		7042	TGFB2	−0.24	0.016	0.9325
		8243	SMC1A	0.75	0.0085	0.98
		9700	ESPL1	0.25	0.010	0.97
		10744	PTTG2	0.46	0.011	0.975
Natural Killer Cell Mediated Cytotoxicity	0.048	355	FAS	−0.42	0.0048	0.9925
		3002	GZMB	−0.23	0.0067	0.985
		3383	ICAM1	−0.32	0.022	0.8975
		3821	KLRC1	−0.43	0.0073	0.97
		3932	LCK	−0.24	0.025	0.875
		5579	PRKCB1	−0.39	0.021	0.8975
		22914	KLRK1	−0.34	0.015	0.9325
T Cell Receptor Signaling Pathway	0.046	917	CD3G	−0.43	0.00097	0.9975
		3702	ITK	−0.18	0.023	0.87
		3932	LCK	−0.24	0.025	0.875
		5788	PTPRC	−0.21	0.024	0.8675
		10892	MALT1	−0.43	0.015	0.905
		29851	ICOS	−0.41	0.018	0.915
Pancreatic Cancer	0.027	1021	CDK6	−0.48	0.010	0.955
		1869	E2F1	0.32	0.0015	1
		1870	E2F2	0.33	0.031	0.8375
		7042	TGFB2	−0.24	0.016	0.9325
		7422	VEGFA	0.15	0.031	0.83
Non Small Cell Lung Cancer	0.0095	1021	CDK6	−0.48	0.010	0.955
		1869	E2F1	0.32	0.0015	1
		1870	E2F2	0.33	0.031	0.8375
		5579	PRKCB1	−0.39	0.021	0.8975
		6256	RXRA	0.45	0.012	0.9525
Primary Immunodeficiency	0.0014	3561	IL2RG	−0.20	0.031	0.8125
		3575	IL7R	−0.23	0.0044	0.995
		3932	LCK	−0.24	0.025	0.875
		5788	PTPRC	−0.21	0.024	0.8675
		29851	ICOS	−0.41	0.018	0.915

The first column contains the names of the pathways; the second column contains the enrichment p-value of the candidate genes to the pathways; the third column (Gene ID) and the forth column (Gene Symbol) contains all candidate genes in the pathways; the fifth column contains the average Cox coefficients of the genes in the 400 runs; the fifth column contains the average p-values of the genes in the 400 runs and the last column contains the stability of the genes in the 400 runs (the ratios of the genes are significant across all the 400 runs). In the table, there are 35 unique genes (some genes may be present at more than one pathways).

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ISSN: 1471-2407

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