Table 2.

Methylation of the HOX genes using the HumanMethylation450 BeadChip and analysis

						Ctrls (n = 6)		MMC (n = 10)
Cluster	Gene	Chr	Illumina ID	P-value <0.05	β-diff>0.05	Mean	SD	Mean	SD
A: Chr.7p14	HOXA2	7	cg06055873	0.016	−0.06	0.32	0.03	0.26	0.04
	HOXA2	7	cg19432993	0.031	−0.12	0.69	0.05	0.57	0.12
	HOXA2	7	cg06166490	0.016	−0.12	0.70	0.06	0.58	0.11
	HOXA2	7	cg04027736	0.022	−0.11	0.61	0.06	0.50	0.11
	HOXA2	7	cg00445443	0.042	−0.10	0.41	0.08	0.31	0.11
		7	cg15037137	0.007	−0.05	0.85	0.02	0.80	0.07
	HOXA4	7	cg25952581	0.042	−0.09	0.45	0.06	0.37	0.11
	HOXA4	7	cg17591595	0.042	−0.08	0.73	0.05	0.65	0.09
	HOXA11	7	cg24709033	0.011	−0.06	0.27	0.03	0.21	0.04
B: Chr.17q21	HOXB5	17	cg01405107	0.042	0.09	0.49	0.05	0.58	0.08
	HOXB6	17	cg09983216	0.016	−0.13	0.55	0.08	0.42	0.10
	HOXB7	17	cg11041817	0.007	−0.29	0.70	0.08	0.41	0.20
	HOXB7	17	cg22622477	0.007	−0.16	0.36	0.06	0.20	0.09
	HOXB7	17	cg07547765	0.007	−0.26	0.71	0.10	0.44	0.18
		17	cg19051015	0.022	−0.09	0.72	0.05	0.63	0.07
	HOXB9	17	cg15117739	0.007	−0.10	0.68	0.04	0.57	0.07
	HOXB9	17	cg12057127	0.042	−0.06	0.72	0.01	0.67	0.07
		17	cg20454400	0.031	−0.06	0.37	0.04	0.31	0.05
		17	cg16654603	0.011	−0.09	0.67	0.02	0.58	0.08
		17	cg02052915	0.016	−0.05	0.36	0.03	0.31	0.04
C: Chr.12q13		12	cg08299265	0.016	−0.06	0.39	0.04	0.33	0.03
		12	cg26643142	0.031	−0.06	0.35	0.03	0.30	0.05
	HOXC4	12	cg18473521	0.011	−0.12	0.43	0.08	0.31	0.07
D: Chr.2q31	HOXD9	2	cg04730882	0.005	−0.07	0.35	0.03	0.28	0.05
		2	cg07783843	0.011	−0.06	0.24	0.02	0.18	0.04
		2	cg05525812	0.007	−0.07	0.25	0.02	0.18	0.05

Nucleotide positions in accord to NCBI build 37/hg19. Selection is performed along both β-value > 0.05 difference and P-value < 0.05; calculated with Wilcoxon Rank-Sum test. The 3 probes in bold are located within the same CpG island at Chr17:46,685,244–46,685,449 within the HOXB7 gene body. This region was selected for the validation study using Sequenom EpiTYPER. β-diff: β-difference; Chr: chromosome; Ctrls: controls; MMC: myelomeningocele.