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Table 1 Summary of differential methylation at individual CpG level and summary of the prioritisation of clusters of DM CpG and associated genes

From: Differential CpG DNA methylation in peripheral naïve CD4+ T-cells in early rheumatoid arthritis patients

  Naïve CD4 Memory CD4 Monocytes
T-cell T-cell
Number (%) of differentially methylated / total probes tested (440 490), p ≤ 0.01 18020 (4.09%) 14197 (3.22%) 6490 (1.47%)
Number (%)* of probes with    
 High significance (p ≤ 0.0001) 561 (3.11%) 440 (3.10%) 130 (2.00%)
 Medium significance (0.0001 < p ≤ 0.001) 2891 (16.04%) 1885 (13.28%) 672 (10.35%)
 Significance (0.001 < p ≤ 0.01) 14568 (80.84%) 11872 (83.62%) 5688 (87.64%)
Number and (%)*of probe associated with    
 Core island 6141 (34.08%) 7120 (50.15%) 1985 (30.59%)
 Shelves/shore island 5873 (32.59%) 3948 (27.81%) 2060 (31.74%)
 Outside of CpG island 6006 (33.33%) 3129 (22.04%) 2445 (37.67%)
 Hypermethylation in RA (%)* 8425 (46.75%) 13218 (93.10%) 3525(54.31%)
 Hypomethylation in RA (%)* 9595 (53.25%) 979 (6.9%) 2965 (45.69%)
Number of probe (%)** associated with an    
 Island/shelve/shore    
  Hypermethylated 1201 (34.79%) 1842 (79.23%) 209 (26.06%)
  Hypomethylated 1111 (32.18%) 114 (4.9%) 310 (38.65%)
 Outside of an island (Open sea)    
  Hypermethylated 176 (5.10%) 299 (12.86%) 190 (23.69%)
  Hypomethylated 964 (27.93%) 70 (3.01%) 93 (11.60%)
DM CpG clusters    
 Number of CpG with a score ≥ 3    
  Hypermethylated 143 305 6
  Hypomethylated 197 0 15
 Number of CpG with a score = 2    
  Hypermethylated 277 414 15
  Hypomethylated 223 7 33
 Score ≥ median (range)    
  Hypermethylated 3.65 (3–9) 3.73 (3–9) 3 (3–4)
  Hypomethylated 4.15 (3–16) Na 3 (3–4)
Corresponding number of genes (all clusters)    
 Hypermethylated 354 600 19
 Hypomethylated 294 5 39
Isolated DM CpG    
 Number of CpG/gene associated with    
  Island/shelve/shore    
   Hypermethylated 121 249 34
   Hypomethylated 139 24 58
  In Open sea    
   Hypermethylated 12 18 14
   Hypomethylated 127 17 13
  1. * (%) of all probes with p ≤ 0.01, ** (%) of all probes with p ≤ 0.001