Genome-Wide DNA Methylation in Mixed Ancestry Individuals with Diabetes and Prediabetes from South Africa

Table 2

KEGG analysis of top ten enrichment score (( value)) values of the significant enrichment pathway.

Pathway ID	Definition	Fisher’s value	Enrichment score	Genes
Hypomethylated diabetes versus control
hsa05143	African trypanosomiasis	0.0073	2.133882	F2RL1//HPR//THOP1
hsa05340	Primary immunodeficiency	0.0086	2.064522	AIRE//CD8A//IGLL1
hsa04640	Hematopoietic cell lineage	0.0200	1.697467	CD1B//CD5//CD8A//CD9
hsa04970	Salivary secretion, Homo sapiens	0.0216	1.665411	ADRB2//CST5//KCNN4//NOS1
hsa00670	One carbon pool by folate	0.0229	1.639815	ATIC//MTFMT
hsa04977	Vitamin digestion and absorption	0.0322	1.490856	SLC19A2//SLC23A1
Hypermethylated diabetes versus control
hsa00910	Nitrogen metabolism	0.0015	2.818773	CA13//CA5B//CA9//CPS1//GLU
				D2
				APLN//CHRNA1//CHRNA5//CH
				RNB3//CNR1//EDN1//EDNRB//
				FSHB//GABRA6//GABRG2//GA
				BRR1//GCG//GHR//GPR156//G
				RIA1//GRM4//HCRTR2//LGR4//
				NMUR2//NPFF//NPY1R//P2RX6
hsa04080	Neuroactive ligand-receptor interaction	0.0207	1.683002	//P2RY14//PLG//RXFP1//TAC4
hsa00524	Butirosin and neomycin biosynthesis	0.0254	1.594577	GCK//HK2
	Glycosaminoglycan biosynthesis, heparan			EXT1//EXTL2//HS3ST5//XYLT
hsa00534	Sulfate/heparin	0.0361	1.441751	1
				CACNB2//EDN1//IGF1//ITGA1//
				ITGB1//MYH6//PRKAG2//PRK
hsa05410	Hypertrophic cardiomyopathy (HCM)	0.0362	1.441099	AG3//TPM1
hsa00750	Vitamin B6 metabolism	0.0368	1.433896	PDXP//PSAT1
hsa04950	Maturity onset diabetes of the young	0.0413	1.384024	GCK//HNF1A//NR5A2//PDX1
Hypomethylated diabetes versus prediabetes
hsa00770	Pantothenate and CoA biosynthesis	0.0137	1.86211	COASY//PANK2
hsa04640	Hematopoietic cell lineage	0.0141	1.850323	CD14//CD1A//CD1B//CD3E
hsa00590	Arachidonic acid metabolism	0.0304	1.516647	CYP2E1//GGT1//PLA2G12A
hsa03320	PPAR signaling pathway	0.0369	1.433374	ACSL4//NR1H3//PCK2
hsa00591	Linoleic acid metabolism	0.0378	1.42268	CYP2E1//PLA2G12A
Hypermethylated diabetes versus prediabetes
hsa05410	Hypertrophic cardiomyopathy (HCM)	0.0063	2.201901	CACNA1S//DMD//ITGA4//MY
				H6//PRKAB2//PRKAG3//TGFB3
				//TNF//TNNI3//TPM4
				ACVR1B//CCR6//CCR8//CX3C
				R1//CXCL1//CXCL9//EDAR//G
				HR//IFNA2//IFNA21//IL18RAP//
				IL3//IL3RA//IL4R//IL9//TGFB3//
				TNF//TNFRSF10D//TNFRSF14//
hsa04060	Cytokine-cytokine receptor interaction	0.0085	2.071022	TNFRSF9//TNFSF18//TNFSF8
hsa03060	Protein export	0.0210	1.678045	SEC61G//SRP9//SRPR//SRPRB
				ADCY4//CACNA1S//DMD//ITG
				A4//MYH6//TGFB3//TNF//TNNI
hsa05414	Dilated cardiomyopathy	0.0251	1.600573	3//TPM4
				ADCY4//ANAPC11//ATF1//ATF
				3//CCNB2//CREM//HLA-
				A//HLA-
				E//IKBKB//KRAS//MAD2L1//M
				RAS//MSX2//NFYB//TGFB3//T
hsa05166	HTLV-I infection	0.0382	1.418455	LN2//TNF//WNT16//WNT5B
				ACSL6//IKBKB//PRKAB2//PRK
hsa04920	Adipocytokine signaling pathway	0.0455	1.342336	AG3//PTPN11//SOCS3//TNF
Hypomethylated prediabetes versus control
hsa00590	Arachidonic acid metabolism	0.0026	2.593265	CYP4F3//CYP4F8//PLA2G2C//P
				LA2G4E
hsa00592	Alpha-linolenic acid metabolism	0.0211	1.676649	PLA2G2C//PLA2G4E
hsa00591	Linoleic acid metabolism	0.0278	1.555232	PLA2G2C//PLA2G4E
				MYLK3//PLA2G2C//PLA2G4E//
hsa04270	Vascular smooth muscle contraction	0.0301	1.521206	RAMP3
hsa04350	TGF-beta signaling pathway	0.0352	1.453226	LEFTY2//SP1//TGFB3
Hypermethylated prediabetes versus control
hsa05202	Transcriptional misregulation in cancer	0.0190	1.720526	CCNT1//ELK4//EYA1//RARA
hsa05221	Acute myeloid leukemia	0.0425	1.371986	CHUK//RARA