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Table 1 Specific genomic features are characterized by hydroxymethylation in brain

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

Probes passing QC on array (%) Prefrontal cortex Cerebellum
Detectable 5hmC sites (%) Enrichment (95 % CI) P value Detectable 5hmC sites (%) Enrichment (95 % CI) P value
All probes (N = 374,094) 37,145 - - 65,563 - -
 CpG island feature
  Island 120,922 (32.3 %) 2,868 (7.7 %) 0.18 (0.17–0.18) <2.53E-294 6,524 (10.0 %) 0.23 (0.23–0.24) <2.53E-294
  Shore 87,312 (23.3 %) 11,934 (32.1 %) 1.55 (1.52–1.59) 2.53E-294 18,544 (28.3 %) 1.30 (1.27–1.32) 1.80E-159
  Shelf 32,912 (8.8 %) 5,434 (14.6 %) 1.78 (1.72–1.83) 3.93E-262 9,958 (15.2 %) 1.86 (1.81–1.90) <2.53E-294
  Outside 124,010 (33.1 %) 16,565 (44.6 %) 1.62 (1.59–1.66) <2.53E-294 29,831 (45.5 %) 1.68 (1.66–1.71) <2.53E-294
  Unannotated 8,938 (2.4 %) 344 (0.9 %) 0.38 (0.34–0.43) 2.99E-91 706 (1.1 %) 0.44 (0.41–0.48) 9.15E-118
 Gene feature
  Intergenic 52,325 (14 %) 4,367 (11.8 %) 0.82 (0.79–0.85) 8.46E-34 7,461 (11.4 %) 0.79 (0.77–0.81) 5.13E-75
  Distal promoter 16,990 (4.5 %) 1,986 (5.3 %) 1.19 (1.13–1.25) 5.16E-12 2,897 (4.4 %) 0.97 (0.93–1.01) 0.166
  Proximal promoter 148,029 (39.6 %) 9,693 (26.1 %) 0.54 (0.53–0.55) <2.53E-294 13,544 (20.7 %) 0.40 (0.39–0.41) <2.53E-294
  Gene body 140,919 (37.7 %) 19,870 (53.5 %) 1.90 (1.86–1.94) <2.53E-294 39,335 (60.0 %) 2.48 (2.44–2.52) <2.53E-294
  Downstream 6,893 (1.8 %) 885 (2.4 %) 1.30 (1.21–1.40) 1.95E-12 1,620 (2.5 %) 1.35 (1.28–1.43) 2.04E-25
  Unannotated 8,938 (2.4 %) 344 (0.9 %) 0.38 (0.34–0.43) 2.99E-91 706 (1.1 %) 0.44 (0.41–0.48) 9.15E-118
 Transcription factor binding site 184,178 (49.2 %) 14,623 (39.4 %) 0.67 (0.66–0.68) 8.40E-291 19,499 (29.7 %) 0.44 (0.43–0.44) <2.53E-294
 Dnase 1 hypersensitivity site 49,903 (13.3 %) 4,449 (12.0 %) 0.88 (0.86–0.91) 7.49E-14 6,227 (9.5 %) 0.68 (0.66–0.70) 5.80E-174
Alternative transcription events (N = 138,640 probes) 14,429 - - 25,582 - -
  A3SS 3,347 (2.4 %) 330 (2.3 %) 0.95 (0.84–1.06) 0.361 700 (2.7 %) 1.14 (1.05–1.24) 2.63E-03
  A5SS 3,364 (2.4 %) 357 (2.5 %) 1.02 (0.91–1.14) 0.712 710 (2.8 %) 1.15 (1.06–1.25) 1.11E-03
  AFE 57,956 (41.8 %) 4,897 (33.9 %) 0.72 (0.69–0.74) 5.07E-76 7,332 (28.7 %) 0.56 (0.54–0.58) <2.53E-294
  ALE 9,026 (6.5 %) 1,353 (9.4 %) 1.49 (1.40–1.58) 1.55E-35 2,554 (10.0 %) 1.59 (1.52–1.67) 5.61E-81
  CE 60,203 (43.4 %) 7,783 (53.9 %) 1.53 (1.47–1.58) 2.14E-128 13,980 (54.6 %) 1.57 (1.53–1.61) 1.17E-239
  CNE 20,661 (14.9 %) 1,592 (11.0 %) 0.71 (0.67–0.75) 1.99E-38 3,149 (12.3 %) 0.80 (0.77–0.83) 3.28E-28
  EI 137 (0.1 %) 19 (0.1 %) 1.33 (0.78–2.16) 0.270 45 (0.2 %) 1.78 (1.24–2.51) 1.39E-03
  II 27,746 (20 %) 3,080 (21.3 %) 1.08 (1.04–1.13) 1.60E-04 4,974 (19.4 %) 0.96 (0.93–1.00) 0.036
  IR 16,175 (11.7 %) 1,550 (10.7 %) 0.91 (0.86–0.96) 8.90E-04 3,025 (11.8 %) 1.02 (0.97–1.06) 0.472
  MXE 13,054 (9.4 %) 1,880 (13 %) 1.44 (1.37–1.52) 8.63E-41 3,221 (12.6 %) 1.39 (1.33–1.44) 6.38E-52
  1. The level of enrichment was determined by Fisher’s exact test. QC, quality control; 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