A metabolome-wide case-control study of african american breast cancer patients

Table 3 Enriched metabolic pathways associated with breast cancer status

Pathway	Pathway size^a	Scenario 1^b		Scenario 2^b		Scenario 3^b		Scenario 4^b		Scenario 5^b		Scenario 6^b		Scenario 7^b
Pathway	Pathway size^a	Overlap size^c	P value^d	Overlap size^c	P value^d	Overlap size^c	P value^d	Overlap size^c	P value^d	Overlap size^c	P value^d	Overlap size^c	P value^d	Overlap size^c	P value^d
Prostaglandin formation from arachidonate	58	8	0.018	7	0.025	9	0.008	7	0.030	10	0.003	6	0.046	9	0.010
Leukotriene metabolism	56	8	0.020	6	0.076	9	0.011	7	0.037	9	0.010	5	0.122	9	0.014
Glycerophospholipid metabolism	48	6	0.040	6	0.025	7	0.016	7	0.009	7	0.015	5	0.052	7	0.019

^a The pathway size is the number of detected empirical compounds for each pathway
^b In scenarios 1 to 7, the cases used to compare healthy controls were: (1) all breast cancer cases, (2) cases without any treatments (chemotherapy, radiotherapy, and surgery) before serum collection, (3) cases with some treatments (chemotherapy, radiotherapy, and surgery) before serum collection, (4) cases with negative lymph nodes, (5) cases with positive lymph nodes, (6) cases with stage I cancer, and (7) cases with stage II/III breast cancer, respectively
^c The overlap size is the number of significant empirical compounds
^d P values calculated by Mummichog were gamma-adjusted P values based on permutation tests by resampling from the reference list