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Table 2 KEGG pathways that enriched with genes that contain DML within their promoters

From: An imprinted rheumatoid arthritis methylome signature reflects pathogenic phenotype

Comparison name

Combined

OA+NL

OA or NL

Comparison description

RA vs (OA or NL) or (OA+NL)

RA vs OA+NL

RA vs OA or NL

Pathway name

EF ( q -value)

# of DMGs (%)

EF ( q -value)

# of DMGs (%)

EF ( q -value)

# of DMGs (%)

Rheumatoid arthritis

2.5 (0.00266)

24 (27.0)

6.5 (1.91e-05)

12 (13.5)

2.3 (0.00467)

22 (24.7)

NOD-like receptor signaling pathway

2.5 (0.00741)

16 (27.6)

5.8 (0.0014)

7 (12.1)

2.3 (0.0374)

14 (24.1)

Cell adhesion molecules (CAMs)

1.8 (0.0294)

25 (19.4)

3.0 (0.0232)

8 (6.2)

1.8 (0.0343)

25 (19.4)

Focal adhesion

1.6 (0.0287)

35 (17.6)

  

1.6 (0.0321)

35 (17.6)

Cytosolic DNA-sensing pathway

  

4.6 (0.0202)

5 (9.6)

  

Cytokine-cytokine receptor interaction

  

2.3 (0.0231)

12 (4.8)

  

Toll-like receptor signaling pathway

1.9 (0.0377)

19 (20.7)

    

Complement and coagulation cascades

2.0 (0.0494)

15 (21.7)

    

Staphylococcus aureus infection

2.9 (0.00379)

16 (31.4)

4.7 (0.019)

5 (9.8)

2.9 (0.00457)

16 (31.4)

Graft-versus-host disease

2.7 (0.0211)

11 (29.7)

10.4 (2.66e-05)

8 (21.6)

2.5 (0.0468)

10 (27.0)

Allograft rejection

2.6 (0.031)

10 (28.6)

9.6 (0.000159)

7 (20.0)

2.7 (0.0389)

10 (28.6)

Leishmaniasis

2.0 (0.0451)

15 (22.1)

4.9 (0.00304)

7 (10.3)

2.1 (0.048)

15 (22.1)

Toxoplasmosis

1.7 (0.0435)

24 (18.8)

3.4 (0.00759)

9 (7.0)

1.7 (0.046)

24 (18.8)

Viral myocarditis

2.6 (0.00392)

19 (27.9)

  

2.6 (0.00457)

19 (27.9)

Dilated cardiomyopathy

2.3 (0.00489)

22 (24.7)

  

2.3 (0.00467)

22 (24.7)

Hypertrophic cardiomyopathy (HCM)

2.3 (0.00487)

21 (25.3)

  

2.2 (0.00904)

20 (24.1)

Aldosterone-regulated sodium reabsorption

2.8 (0.00761)

13 (31.0)

  

2.9 (0.00814)

13 (31.0)

Influenza A

1.7 (0.0308)

29 (18.4)

4.0 (0.000283)

13 (8.2)

  

Type II diabetes mellitus

2.5 (0.0185)

13 (27.7)

  

2.6 (0.0203)

13 (27.7)

Carbohydrate digestion and absorption

2.6 (0.0225)

12 (27.9)

  

2.4 (0.0474)

11 (25.6)

Type I diabetes mellitus

  

8.2 (0.000269)

7 (17.1)

  

Asthma

  

10.3 (0.000274)

6 (21.4)

  

Tuberculosis

  

3.8 (0.000386)

13 (7.9)

  

Antigen processing and presentation

  

5.7 (0.000668)

8 (11.9)

  

Phagosome

  

3.7 (0.00131)

11 (7.7)

  

Autoimmune thyroid disease

  

6.9 (0.00152)

6 (14.3)

  

Intestinal immune network for IgA production

  

6.3 (0.00233)

6 (13.0)

  

Chagas disease (American trypanosomiasis)

2.0 (0.0206)

22 (21.4)

    

Prion diseases

  

5.5 (0.0246)

4 (11.4)

  

African trypanosomiasis

2.6 (0.031)

10 (28.6)

    
  1. KEGG pathways that are found as significantly enriched (q < 0.05) in three comparisons are shown. Eight pathways especially relevant to RA are placed in the top part of the table. Within each section, the number of significant comparisons orders the pathways. If multiple pathways have the same number of comparison then an average q values is used for ordering. # denotes the number of DMGs in the selected pathway.
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Genome Medicine

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