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Table 3 The 1,000 top tissue-specific hydroxymethylated positions (TS-HMPs) between the prefrontal cortex and cerebellum are enriched in distinct genomic regions

From: Variation in 5-hydroxymethylcytosine across human cortex and cerebellum

  Loci with detectable 5hmC in brain (%) Top 1,000 loci with tissue-specific differences
Sites with detectable 5hmC (%) Enrichment (95 % CI) P value
All probes (N = 79,263) 1,000 - -
 CpG island feature
  Island 7,837 (9.9 %) 317 (31.7 %) 4.23 (3.68–4.85) 6.37E-79
  Shore 22,593 (28.5 %) 209 (20.9 %) 0.66 (0.57–0.77) 6.20E-08
  Shelf 11,674 (14.7 %) 92 (9.2 %) 0.59 (0.47–0.73) 2.64E-07
  Outside 36,342 (45.8 %) 381 (38.1 %) 0.73 (0.64–0.83) 9.82E-07
  Unannotated 817 (1.0 %) 1 (0.1 %) 0.10 (0.00–0.54) 7.00E-04
 Gene feature
  Intergenic 9,604 (12.1 %) 132 (13.2 %) 1.10 (0.91–1.33) 0.306
  Distal promoter 3,703 (4.7 %) 25 (2.5 %) 0.52 (0.34–0.78) 6.30E-04
  Proximal promoter 16,979 (21.4 %) 121 (12.1 %) 0.50 (0.41–0.61) 3.32E-14
  Gene body 46,238 (58.3 %) 690 (69.0 %) 1.59 (1.39–1.82) 5.15E-12
  Downstream 1,922 (2.4 %) 31 (3.1 %) 1.29 (0.87–1.85) 0.178
  Unannotated 817 (1.0 %) 1 (0.1 %) 0.10 (0.00–0.54) 7.00E-04
 Transcription factor binding site 25,482 (32.1 %) 125 (12.5 %) 0.30 (0.25–0.36) 1.30E-46
 Dnase 1 hypersensitivity site 8,155 (10.3 %) 280 (28.0 %) 3.39 (2.94–3.91) 3.51E-54
Alternative transcription events (N = 30,659) 404 - -
  A3SS 798 (2.6 %) 14 (3.5 %) 1.34 (0.72–2.29) 0.270
  A5SS 827 (2.7 %) 17 (4.2 %) 1.58 (0.91–2.59) 0.087
  AFE 9,159 (29.9 %) 92 (22.8 %) 0.69 (0.54–0.88) 1.77E-03
  ALE 3,017 (9.8 %) 40 (9.9 %) 1.01 (0.71–1.40) 0.933
  CE 16,604 (54.2 %) 202 (50.0 %) 0.85 (0.69–1.04) 0.097
  CNE 3,755 (12.2 %) 69 (17.1 %) 1.48 (1.12–1.92) 4.70E-03
  EI 50 (0.2 %) 1 (0.2 %) 1.52 (0.04–8.91) 0.487
  II 6,003 (19.6 %) 59 (14.6 %) 0.70 (0.52–0.93) 0.011
  IR 3,529 (11.5 %) 54 (13.4 %) 1.19 (0.87–1.59) 0.240
  MXE 3,814 (12.4 %) 39 (9.7 %) 0.75 (0.53–1.05) 0.095
  1. The level of enrichment of the top 1,000 loci was determined by Fisher’s exact test. 5hmC, 5-hydroxymethylcytosine; CI, confidence interval; A3SS, alternative 3’ splice site; A5SS, alternative 5’ splice site; AFE, alternative first exon; ALE, alternative last exon; CE, cassette exon; CNE, constitutive exon; EI, exon isoforms; II, intron isoforms; IR, intron retention; MXE, mutually exclusive exon