Table 4.

Examples of gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of hypomethylated and hypermethylated genes in rheumatoid arthritis (RA)

Analysis type	Marginal probability (GO)	p value (KEGG)	Name
RA hypomethylated
GO	0.998		Transcription coactivator activity
GO	0.985		ATPase binding
GO	0.956		PcG protein complex
GO	0.922		Positive regulation of transcription from RNA polymerase II promoter
GO	0.820		Extrinsic to plasma membrane
GO	0.811		Transcription factor binding
GO	0.788		G-protein activated inward rectifier potassium channel activity
GO	0.762		Regulation of exocytosis
GO	0.710		Nuclear hormone receptor binding
GO	0.592		Ubiquitin thiolesterase activity
GO	0.554		Phospholipase C activity
GO	0.536		External side of plasma membrane
GO	0.523		Actin cytoskeleton
GO	0.511		Biological adhesion
KEGG		0.007	Focal adhesion
KEGG		0.007	Glycosphingolipid biosynthesis—lacto and neolacto series
KEGG		0.007	ECM–receptor interaction
KEGG		0.014	Leukocyte transendothelial migration
KEGG		0.034	Protein digestion and absorption
KEGG		0.044	Adipocytokine signalling pathway
KEGG		0.062	Cell adhesion molecules
KEGG		0.085	Nitrogen metabolism
RA hypermethylated
GO	0.771		Golgi apparatus
GO	0.766		Cell surface receptor linked signalling pathway
GO	0.603		Binding
KEGG		0.058	ErbB signalling pathway
KEGG		0.095	Fc ε RI signalling pathway
KEGG		0.095	mTOR signalling pathway
KEGG		0.095	Adipocytokine signalling pathway

The significance of GO terms and KEGG pathways were measured using marginal probabilities and p values, respectively. GO terms and KEGG pathways were shown if they had a marginal probability >0.5 or p values <0.1, respectively. GO terms and KEGG pathways which are irrelevant to RA were omitted from the table but are included in the supplementary information.