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Table 2 TFBS enrichment analysis points to altered TFBS occupancy as a mechanism underlying some examples of tissue-specific and tissue-invariant DS-DM

From: Trans effects of chromosome aneuploidies on DNA methylation patterns in human Down syndrome and mouse models

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

  1. 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
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Genome Biology

ISSN: 1474-760X

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