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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 CD4Memory CD4Monocytes
T-cellT-cell
Number (%) of differentially methylated / total probes tested (440 490), p ≤ 0.0118020 (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 island6141 (34.08%)7120 (50.15%)1985 (30.59%)
 Shelves/shore island5873 (32.59%)3948 (27.81%)2060 (31.74%)
 Outside of CpG island6006 (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   
  Hypermethylated1201 (34.79%)1842 (79.23%)209 (26.06%)
  Hypomethylated1111 (32.18%)114 (4.9%)310 (38.65%)
 Outside of an island (Open sea)   
  Hypermethylated176 (5.10%)299 (12.86%)190 (23.69%)
  Hypomethylated964 (27.93%)70 (3.01%)93 (11.60%)
DM CpG clusters   
 Number of CpG with a score ≥ 3   
  Hypermethylated1433056
  Hypomethylated197015
 Number of CpG with a score = 2   
  Hypermethylated27741415
  Hypomethylated223733
 Score ≥ median (range)   
  Hypermethylated3.65 (3–9)3.73 (3–9)3 (3–4)
  Hypomethylated4.15 (3–16)Na3 (3–4)
Corresponding number of genes (all clusters)   
 Hypermethylated35460019
 Hypomethylated294539
Isolated DM CpG   
 Number of CpG/gene associated with   
  Island/shelve/shore   
   Hypermethylated12124934
   Hypomethylated1392458
  In Open sea   
   Hypermethylated121814
   Hypomethylated1271713
  1. * (%) of all probes with p ≤ 0.01, ** (%) of all probes with p ≤ 0.001