TABLE 3.

Selected canonical pathways and gene ontology groups modulated by administration of vitamin D with or without calcium supplementation¹

	FDR-q val	↑ or ↓	Database
WD + vitamin D
CHEMOKINE_SIGNALING_PATHWAY	<0.000	↑	REACTOME
LEISHMANIA_INFECTION	<0.000	↑	KEGG
INTERFERON_ALPHA_BETA_SIGNALING	<0.000	↑	REACTOME
CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION	<0.000	↑	KEGG
NOD_LIKE_RECEPTOR_SIGNALING_PATHWAY	<0.000	↑	KEGG
ASTHMA	<0.000	↑	KEGG
IL12_2PATHWAY	<0.000	↑	PID
G1_S_TRANSITION	<0.000	↑	REACTOME
INTEGRIN1_PATHWAY	<0.000	↑	PID
INTERFERON_GAMMA_SIGNALING	<0.000	↑	REACTOME
CELL_ADHESION_MOLECULES_CAMS	<0.000	↑	KEGG
ANTIGEN_PROCESSING_AND_PRESENTATION	<0.001	↑	KEGG
MITOTIC_G1_G1_S_PHASES	<0.001	↑	REACTOME
IL23PATHWAY	<0.001	↑	PID
CHEMOKINE_ACTIVITY	<0.000	↑	GO
CYTOKINE_ACTIVITY	<0.000	↑	GO
INFLAMMATORY_RESPONSE	<0.000	↑	GO
IMMUNE_RESPONSE	<0.000	↑	GO
EXTRACELLULAR_REGION	<0.001	↑	GO
REGULATION_OF_CELL_CYCLE	<0.001	↑	GO
WD + vitamin D + 2 g Ca/d
CHEMOKINE_RECEPTORS_BIND_CHEMOKINES	<0.001	↑	REACTOME
CHEMOKINE_ACTIVITY	0.011	↑	GO
IMMUNE_RESPONSE	0.049	↑	GO
PEROXISOME	<0.001	↓	KEGG
EXCRETION	<0.001	↓	GO
PEROXISOME	0.005	↓	GO
SECRETION	0.012	↓	GO

¹The full list is shown in Supplemental Table 4. The WD was designed as high in fat content (40% of calories) and low in vitamin D (estimated as ∼150–200 IU/d) and calcium (∼400 mg/d). We determined the effects of vitamin D (0.5 μg calcitriol) with or without 2 g supplemental Ca/d on rectosigmoid mucosal gene expression. Note that most of the pathways or processes changed by vitamin D occurred in immune or inflammatory genes with some contribution of cell cycle genes and extracellular matrix protein genes. Most of these effects of vitamin D were abrogated by calcium supplementation. FDR-q val, false discovery rate adjusted significance (q value); WD, Western-style diet; ↑, increase; ↓, decrease.