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Table 4 Enrichment test for association between genes silenced by X-inactivation and DMRs, and genes that escape from X-inactivation and gaps between DMRs. Only CpGs on the X-chromosome overlapping genes are used in the enrichment test

From: DMRscaler: a scale-aware method to identify regions of differential DNA methylation spanning basepair to multi-megabase features

Method

Odds ratio (95% CI)

p-value (Fisher’s Exact)

DMRscaler

Layer 1: 4 adj CpGs

7.57 (6.38–8.99)

1.04e-134

Layer 2: 8 adj CpGs

7.24 (6.07–8.65)

5.93e-100

Layer 3: 16 adj CpGs

51.99 (30.38–90.33)

4.34e-77

Layer 4: 32 adj CpGs

160.44 (25.42–6,396.92)

6.59e-18

Layer 5: 64 adj CpGs

0 (0–319.59)

1

bumphunter

Default: maxGap = 1 kb

14 (11.18–17.61)

7.00E-185

maxGap = 1 Mb

15 (11.95–18.94)

5.36E-193

comb-p

dist = 1 kb, step = 100 bp

2.07 (1.63–2.62)

5.72E-09

dist = 1 Mb, step = 100 kb

0 (0–Inf)

1

DMRcate

Default: lambda = 1 kb, C = 2

1.27 (1.03–1.57)

0.023608

Lambda = 1 Mb, C = 2000

0 (0–43.86)

1