Table 1. Number of differentially-enriched functions and pathways in Ingenuity Pathway Analysis (IPA) using different false discovery rate (FDR) correction thresholds of the raw P-values.

	FDR cut off for Functions						FDR cut off for Pathways						DEG
Comparison	0.05	0.10	0.30	0.50	0.70	1.00	0.05	0.10	0.30	0.50	0.70	1.00	Overall	Eligible IPA
–15 vs. –30	1	1	1	1	39	39	0	0	0	3	3	3	1320	696
1 vs. –30	0	0	0	0	0	42	0	0	8	12	29	38	3688	2027
15 vs. –30	0	0	0	1	39	39	0	0	0	0	0	10	2703	1507
30 vs. –30	0	0	0	0	40	40	0	0	0	2	2	2	3242	1877
60 vs. –30	0	0	0	0	0	39	0	1	1	2	10	32	3980	2175
120 vs. –30	0	0	0	0	0	37	0	0	0	0	8	9	3821	2092
240 vs. –30	1	6	21	36	36	36	0	1	2	13	21	91	1502	874
300 vs. –30	0	0	0	0	40	40	0	1	1	3	3	29	1522	843
1 vs. –15	0	0	7	10	40	40	0	0	0	9	18	38	2038	1198
15 vs. 1	0	0	3	42	42	42	0	0	0	0	0	0	1326	753
30 vs. 15	0	0	41	41	41	41	0	0	0	69	110	112	235	146
60 vs. 30	0	0	0	44	44	44	2	2	17	38	81	97	378	211
120 vs. 60	0	0	0	43	43	43	0	0	0	1	1	5	327	184
240 vs. 120	0	0	0	0	0	45	0	0	0	0	0	0	2027	1107
300 vs. 240	0	0	0	41	41	41	1	2	5	5	52	83	356	215

Reported is the number of functions, pathways and DEG enriched at the specified FDR cut-off. Legend: FDR = false discovery rate cut-off applied in the function/pathway analysis; DEG = differentially expressed genes, with “Overall” denoting the total number of DEG and “Eligible in IPA” the number of DEG eligible for function/pathway analysis in IPA.