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Table 2 The most hydroxymethylated loci in prefrontal cortex and cerebellum are enriched in distinict genomic regions

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

Loci with detectable 5hmC in brain (%) 1,000 loci with highest 5hmC in prefrontal cortex 1,000 loci with highest 5hmC in cerebellum
Detectable 5hmC sites (%) Enrichment (95 % CI) P value Detectable 5hmC sites (%) Enrichment (95 % CI) P value
All probes (N = 79,263) 1,000 - - 1,000 - -
 CpG island feature
  Island 7,837 (9.9 %) 121 (12.1 %) 1.25 (1.03–1.52) 0.022 275 (27.5 %) 3.46 (2.99–3.99) 7.01E-55
  Shore 22,593 (28.5 %) 472 (47.2 %) 2.24 (1.97–2.55) 3.19E-35 276 (27.6 %) 0.96 (0.83–1.10) 0.549
  Shelf 11,674 (14.7 %) 93 (9.3 %) 0.59 (0.47–0.74) 4.29E-07 121 (12.1 %) 0.80 (0.65–0.97) 0.019
  Outside 36,342 (45.8 %) 307 (30.7 %) 0.52 (0.46–0.60) 3.37E-22 326 (32.6 %) 0.57 (0.50–0.65) 2.94E-17
  Unannotated 817 (1.0 %) 7 (0.7 %) 0.68 (0.27–1.41) 0.426 2 (0.2 %) 0.19 (0.02–0.70) 3.94E-03
 Gene feature
  Intergenic 9,604 (12.1 %) 89 (8.9 %) 0.71 (0.56–0.88) 1.48E-03 74 (7.4 %) 0.58 (0.45–0.74) 1.56E-06
  Distal promoter 3,703 (4.7 %) 46 (4.6 %) 0.98 (0.71–1.33) 1.000 19 (1.9 %) 0.40 (0.24–0.62) 4.88E-06
  Proximal promoter 16,979 (21.4 %) 365 (36.5 %) 2.11 (1.85–2.40) 3.10E-27 206 (20.6 %) 0.95 (0.81–1.11) 0.561
  Gene body 46,238 (58.3 %) 474 (47.4 %) 0.64 (0.57–0.73) 5.30E-12 670 (67.0 %) 1.45 (1.27–1.66) 2.60E-08
  Downstream 1,922 (2.4 %) 19 (1.9 %) 0.78 (0.47–1.23) 0.350 29 (2.9 %) 1.20 (0.80–1.74) 0.351
  Unannotated 817 (1.0 %) 7 (0.7 %) 0.68 (0.27–1.41) 0.426 2 (0.2 %) 0.19 (0.02–0.70) 3.94E-03
 Transcription factor binding Site 25,482 (32.1 %) 545 (54.5 %) 2.53 (2.22–2.87) 2.57E-47 383 (38.3 %) 1.31 (1.15–1.49) 4.97E-05
 Dnase 1 hypersensitivity site 8,155 (10.3 %) 150 (15 %) 1.54 (1.28–1.84) 3.95E-06 143 (14.3 %) 1.45 (1.21–1.74) 8.42E-05
Alternative transcription events (N = 30,659 probes) 398 - - 451 - -
  A3SS 798 (2.6 %) 8 (2.0 %) 0.77 (0.33–1.54) 0.632 22 (4.9 %) 1.92 (1.18–2.96) 6.74E-03
  A5SS 827 (2.7 %) 12 (3.0 %) 1.12 (0.57–1.90) 0.640 17 (3.8 %) 1.41 (0.81–2.30) 0.185
  AFE 9,159 (29.9 %) 158 (39.7 %) 1.55 (1.25–1.90) 3.41E-05 112 (24.8 %) 0.78 (0.62–0.96) 0.020
  ALE 3,017 (9.8 %) 27 (6.8 %) 0.67 (0.43–0.99) 0.041 46 (10.2 %) 1.04 (0.75–1.42) 0.811
  CE 16,604 (54.2 %) 185 (46.5 %) 0.74 (0.60–0.90) 2.37E-03 208 (46.1 %) 0.72 (0.60–0.88) 7.17E-04
  CNE 3,755 (12.2 %) 53 (13.3 %) 1.10 (0.81–1.48) 0.490 62 (13.7 %) 1.14 (0.86–1.50) 0.347
  EI 50 (0.2 %) 1 (0.3 %) 1.54 (0.04–9.04) 0.482 2 (0.4 %) 2.73 (0.32–10.43) 0.174
  II 6,003 (19.6 %) 89 (22.4 %) 1.18 (0.92–1.50) 0.163 87 (12.3 %) 0.98 (0.77–1.25) 0.952
  IR 3,529 (11.5 %) 63 (15.8 %) 1.45 (1.08–1.90) 0.011 80 (17.7 %) 1.66 (1.28–2.12) 1.08E-04
  MXE 3,814 (12.4 %) 43 (10.8 %) 0.85 (0.61–1.17) 0.259 35 (7.8 %) 0.59 (0.41–0.84) 1.90E-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