Table 2.

TFBS enrichment analysis points to altered TFBS occupancy as a mechanism underlying some examples of tissue-specific and tissue-invariant DS-DM

Loci with DS-DM shared across multiple tissues	Encode motifs	Odds ratio (enrichment)	P value	FDR	Count in DS-DM CpGs	Count in background	Percentage of DS-DM CpGs	Percentage of background CpGs
54 DS_DM CpGs shared by all brain tissues and cell types: hypermethylated set (diff. > 0.15, p > 0.005)	CTCF_ext	8.03	1.09E-09	6.65E-08	10	6989	14.29	2.04
	MEF2	22.33	1.75E-09	6.65E-08	4	933	5.71	0.27
	CTCF	2.34	0.0015	0.039	19	47,093	27.14	13.72
	USF	2.66	0.035	0.67	5	9661	7.14	2.81
47 DS-DM CpGs shared by all tissues and cell types (including T cells): hypermethylated set (diff. > 0.15, p < 0.005)	CTCF_ext	9.09	1.57E-10	1.20E-08	10	6989	15.87	2.04
	MEF2	24.98	5.10E-10	1.94E-08	4	933	6.35	0.27
	CTCF	2.32	0.0030	0.075	17	47,093	26.98	13.72
	USF	2.98	0.019	0.37	5	9661	7.94	2.81

TFBS enrichment among loci with DS-DM shared across multiple tissues, showing a strong enrichment in CTCF binding motif instances (as identified in ENCODE) in 200-bp windows containing the DS-DM CpGs. For the full TFBS enrichment results in all DS-DM sets see Table S14b in Additional file 2