Novel insights into systemic sclerosis using a sensitive computational method to analyze whole-genome bisulfite sequencing data

Table 2 Comparison of numbers of regions identified by the two methods used for DMR and DMG detection

Method used	# of CpG Regions	# of CpG regions with ≥ 60 CpGs	# of DMRs	# of DMRs with ≥ 60 CpGs	# of DMGs	Mean # of CpG sites per CpG Region	Mean # of CpG sites per DMR
SOMNiBUS (p < 6.05e−06; FWER < 0.05)	8268	8268	131	131	125	108.3	124.5
SOMNiBUS (p < 0.05)	8268	8268	1228	1228	1183	108.3	113.2
Bumphunter (q-value < 0.05)	821,929	0	599	0	340	1.1	2.5

For SOMNiBUS, the FWER of 0.05 was estimated by a Bonferroni correction for the number of regions analyzed: 0.05/8268 = 6.05e−06. For bumphunter, the software uses permutations to estimate genome-wide false discovery rates, and [27] reported results for q-values < 0.05

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