. 2016 Apr 22;17:298. doi: 10.1186/s12864-016-2617-2

Table 1.

Number of differentially methylated and H3K4me3-enriched CpG islands (CGIs) in hepatic DNA of control A/J and WSB/EiJ mice

Location	MeDIP				ChIP-on-chip
Location	Strain	Number of hypo- or hyper-methylated CGIs^a	Proportion hyper-methylated CGIs	z-test^c	Strain	Number of CGIs with decreased or increased H3K4me3 enrichment^b	Proportion with increased H3K4me3 enrichment	z-test^c
Promoter	A/J	1254	0.40	P < 0.001	A/J	2578	0.47	P < 0.001
Promoter	WSB/EiJ	1254	0.10	P < 0.001	WSB/EiJ	2578	0.41	P < 0.001
Gene Body	A/J	2371	0.52	P < 0.001	A/J	4828	0.52	P = 0.015
Gene Body	WSB/EiJ	2371	0.14	P < 0.001	WSB/EiJ	4828	0.54	P = 0.015
Downstream	A/J	128	0.57	P < 0.001	A/J	201	0.70	P > 0.05
Downstream	WSB/EiJ	128	0.11	P < 0.001	WSB/EiJ	201	0.66	P > 0.05
Divergent promoter	A/J	147	0.37	P < 0.001	A/J	341	0.35	P > 0.05
Divergent promoter	WSB/EiJ	147	0.07	P < 0.001	WSB/EiJ	341	0.30	P > 0.05
Total	A/J	3900	0.48	P < 0.001	A/J	7948	0.50	P > 0.05
Total	WSB/EiJ	3900	0.12	P < 0.001	WSB/EiJ	7948	0.49	P > 0.05

^aCGI fragments with a negative Z score and p < 0.05 were considered being significantly hypomethylated, and CGI fragments with a positive Z score and p < 0.05 were considered being significantly hypermethylated

^bThe H3K4me3 enrichment was considered to be significant if the CGI fragments ratio IP/input DNA p value was < 0.05

^cComparisons in the extent of hypermethylation and H3K4me3 enrichment between A/J and WSB/EiJ mice were conducted by one-tailed z-tests