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Table 4 The most variable hydroxymethylated loci in 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 most variable loci in prefrontal cortex Top 1,000 most variable loci in cerebellum
Sites with detectable 5hmC (%) Enrichment (95 % CI) P value Sites with detectable 5hmC (%) Enrichment (95 % CI) P value
All probes (N = 79,263) 1,000 - - 1,000 - -
 CpG island feature
  Island 7,837 (9.9 %) 159 (15.9 %) 1.72 (1.44–2.05) 4.037E-09 301 (30.1 %) 3.92 (3.41–4.51) 2.41E-69
  Shore 22,593 (28.5 %) 270 (27.0 %) 0.93 (0.80–1.07) 0.307 171 (17.1 %) 0.52 (0.44–0.61) 9.25E-17
  Shelf 11,674 (14.7 %) 107 (10.7 %) 0.69 (0.56–0.85) 2.23E-04 134 (13.4 %) 0.90 (0.74–1.08) 0.261
  Outside 36,342 (45.8 %) 376 (37.6 %) 0.71 (0.62–0.81) 1.82E-07 281 (28.1 %) 0.46 (0.40–0.53) 3.04E-30
  Unannotated 817 (1.0 %) 88 (8.8 %) 9.26 (7.28–11.67) 4.97E-50 113 (11.3 %) 12.23 (9.85–15.09) 1.10E-74
 Gene feature
  Intergenic 9,604 (12.1 %) 99 (9.9 %) 0.80 (0.64–0.98) 0.032 80 (8.0 %) 0.63 (0.49–0.79) 3.86E-05
  Distal promoter 3,703 (4.7 %) 36 (3.6 %) 0.76 (0.53–1.06) 0.113 30 (3.0 %) 0.63 (0.42–0.91) 0.010
  Proximal promoter 16,979 (21.4 %) 172 (17.2 %) 0.76 (0.64–0.90) 1.10E-03 113 (11.3 %) 0.47 (0.38–0.57) 1.03E-16
  Gene body 46,238 (58.3 %) 583 (58.3 %) 1.00 (0.88–1.14) 1.000 642 (64.2 %) 1.28 (1.12–1.46) 1.78E-04
  Downstream 1,922 (2.4 %) 22 (2.2 %) 0.91 (0.56–1.38) 0.756 22 (22.0 %) 0.91 (0.56–1.38) 0.756
  Unannotated 817 (1.0 %) 88 (8.8 %) 9.26 (7.28–11.67) 4.97E-50 113 (11.3 %) 12.23 (9.85–15.09) 1.10E-74
 Transcription factor binding site 25,482 (32.1 %) 298 (29.8 %) 0.90 (0.78–1.03) 0.117 242 (24.2 %) 0.67 (0.58–0.78) 4.57E-08
 Dnase 1 hypersensitivity site 8,155 (10.3 %) 77 (7.7 %) 0.73 (0.57–0.92) 6.33E-03 61 (6.1 %) 0.57 (0.43–0.74) 4.56E-06
Alternative transcription events (N = 30,659) 385 - - 418 - -
  A3SS 798 (2.6 %) 15 (3.9 %) 1.52 (0.84–2.55) 0.144 15 (3.6 %) 1.39 (0.77–2.34) 0.214
  A5SS 827 (2.7 %) 10 (2.6 %) 0.96 (0.46–1.80) 1.000 17 (4.1 %) 1.53 (0.88–2.49) 0.094
  AFE 9,159 (29.9 %) 103 (26.8 %) 0.86 (0.68–1.08) 0.197 82 (19.6 %) 0.57 (0.44–0.73) 2.55E-06
  ALE 3,017 (9.8 %) 36 (9.4 %) 0.95 (0.65–1.34) 0.863 38 (9.1 %) 0.92 (0.64–1.28) 0.679
  CE 16,604 (54.2 %) 200 (51.9 %) 0.92 (0.74–1.13) 0.410 187 (44.7 %) 0.69 (0.56–0.84) 1.38E-04
  CNE 3,755 (12.2 %) 60 (15.6 %) 1.32 (0.98–1.75) 0.051 86 (20.6 %) 1.86 (1.44–2.37) 1.95E-06
  EI 50 (0.2 %) 1 (0.3 %) 1.59 (0.04–9.35) 0.471 2 (0.5 %) 2.94 (0.35–11.27 0.155
  II 6,003 (19.6 %) 74 (19.2 %) 0.98 (0.75–1.27) 0.897 69 (16.5 %) 0.81 (0.62–1.06) 0.121
  IR 3,529 (11.5 %) 41 (10.6 %) 0.92 (0.64–1.27) 0.688 68 (16.3 %) 1.49 (1.13–1.95) 4.24E-03
  MXE 3,814 (12.4 %) 40 (10.4 %) 0.82 (0.57–1.14) 0.244 31 (7.4 %) 0.56 (0.38–0.82) 1.26E-03
  1. The level of enrichment of the top 1,000 loci in each brain region 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