Table 1.

Optimal evolutionary models of DNA methylation and gene expression for the four gene families in controls (promoter methylation vs. gene expression ∣ gene body methylation vs. gene expression)

Disease	Chemokine receptor	TNF receptor	TGF– β	IL17
Allergy	OUOU ∣ OUOU	OUOU ∣ OUOU	OUOU ∣ OUOU	OUOU ∣ OUOU
Asthma	OUOU ∣ OUOU	OUOU ∣ OUOU	OUOU ∣ OUOU	OUOU ∣ OUOU
CFS	OUOU ∣ OUOU	OUOU ∣ OUOU	OUOU ∣ OUOU	OUOU ∣ OUOU
Colitis	BM ∣ BM	OUOU ∣ OUOU	OUOU ∣ OUOU	OUOU ∣ OUOU
Colon Cancer	OUOU ∣ OUOU	OUOU ∣ BM	OUOU ∣ OUOU	OUOU ∣ OUOU
Crohn	OUOU ∣ OUOU	BM ∣ OUOU	OUOU ∣ OUOU	OUOU ∣ OUOU
RA	OUBM ∣ OUOU	OUOU ∣ OUOU	OUOU ∣ OUOU	BM ∣ OUOU
SLE	OUOU ∣ OUOU	OUOU ∣ OUOU	OUOU ∣ OUOU	OUOU ∣ OUOU
T2D	OUOU ∣ OUOU	OUOU ∣ OUOU	OUOU ∣ OUOU	BM ∣ BM

OUOU: bivariate OU model, both methylation and expression follow OU model; BM: Brownian Motion model, both methylation and expression follow BM model; OUBM: methylation and expression follow different models