TABLE 2.

GO biological processes inhibited by HDL but not by cholesterol-cyclodextrin

GO ID	Term	N Genes in Pathway	Expected N Significant Genes	N Significant OxPAPC	POxPAPC	POxPAPC+HDL	POxPAPC+CHOL
GO:0051145	Smooth muscle cell differentiation	22	5.82	17	1.60E-06	NS	0.00015
GO:0007049	Cell cycle	1,137	300.9	373	2.50E-06	NS	4.20E-06
GO:0001568	Blood vessel development	341	90.24	139	6.90E-06	NS	1.40E-05
GO:0042326	Negative regulation of phosphorylation	155	41	68	1.80E-06	NS	5.00E-06
GO:0001944	Vasculature development	358	94.74	146	1.00E-05	NS	9.20E-06
GO:2000112	Regulation of cellular macromolecule biosynthesis	2,227	589.37	701	4.10E-05	NS	0.00017
GO:0031349	Positive regulation of defense response	153	40.49	69	4.40E-05	NS	NS
GO:0006809	Nitric oxide biosynthetic process	35	9.26	22	6.70E-05	NS	0.00046
GO:0001816	Cytokine production	263	69.6	105	6.90E-05	NS	0.0008
GO:2000113	Negative regulation of cellular macromolecule biosynthetic process	633	167.52	223	0.00014	NS	0.00033

Enrichment of GO terms was assessed using topGO R package. Biological processes that showed significant enrichment in OxPAPC-treated sample but not in OxPAPC+HDL-treated sample were ranked by enrichment P value in OxPAPC-treated sample. Top 10 biological processes are shown (see supplementary Table III for the full list). Notably, 9 of the 10 most significant process reversed by HDL were not reversed by cholesterol loading. CHOL, cholesterol.