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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