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

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