From: Variation in 5-hydroxymethylcytosine across human cortex and cerebellum
Probes passing QC on array (%) | Prefrontal cortex | Cerebellum | |||||
---|---|---|---|---|---|---|---|
Detectable 5hmC sites (%) | Enrichment (95Â % CI) | P value | Detectable 5hmC sites (%) | Enrichment (95Â % 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 |