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Table 2 Biological pathways associated with SSKB genes

From: Text-mining applied to autoimmune disease research: the Sjögren’s syndrome knowledge base

Rank

PATHWAY

SSKB Genes

ENRICHMENT

Raw P

Adjust P

1

Allograft rejection

23

76.02

3.62E-39

6.82E-38

2

Intestinal immune network for IgA production

27

67.82

7.26E-44

2.05E-42

3

Asthma

14

58.61

4.14E-22

2.75E-21

4

Type I diabetes mellitus

20

57.09

9.13E-31

9.38E-30

5

Graft-versus-host disease

18

53.83

3.21E-27

2.79E-26

6

Autoimmune thyroid disease

22

52.13

1.29E-32

1.82E-31

7

Primary immunodeficiency

14

50.24

6.38E-21

3.79E-20

8

Hematopoietic cell lineage

33

47.1

1.39E-46

5.24E-45

9

Toll-like receptor signaling pathway

37

46.01

1.13E-51

6.38E-50

10

Apoptosis

25

35.68

5.55E-32

6.97E-31

11

NOD-like receptor signaling pathway

17

34.44

7.61E-22

4.78E-21

12

Amyotrophic lateral sclerosis (ALS)

14

33.18

5.81E-18

2.85E-17

13

Other glycan degradation

4

31.4

6.67E-06

1.24E-05

14

Cytokine-cytokine receptor interaction

66

31.05

5.91E-79

6.68E-77

15

T cell receptor signaling pathway

26

30.24

4.12E-31

4.66E-30

16

RIG-I-like receptor signaling pathway

17

30.07

9.98E-21

5.64E-20

17

Cell adhesion molecules (CAMs)

32

29.99

6.40E-38

1.03E-36

18

Bladder cancer

10

29.9

1.06E-12

3.24E-12

19

Viral myocarditis

17

29.25

1.68E-20

9.04E-20

20

Cytosolic DNA-sensing pathway

13

29.16

5.78E-16

2.42E-15

21

Pancreatic cancer

15

26.17

1.88E-17

8.50E-17

22

Small cell lung cancer

16

23.92

7.32E-18

3.45E-17

23

Glycosaminoglycan degradation

4

23.92

2.13E-05

3.65E-05

24

Natural killer cell mediated cytotoxicity

25

22.92

1.06E-26

8.56E-26

25

ErbB signaling pathway

13

22.16

2.51E-13

8.86E-13

26

Epithelial cell signaling in Helicobacter pylori infection

12

22.16

2.64E-13

9.04E-13

27

Complement and coagulation cascades

12

21.84

3.17E-13

1.05E-12

28

B cell receptor signaling pathway

13

21.77

3.38E-14

1.23E-13

29

Prion diseases

6

21.53

3.27E-07

6.84E-07

30

Antigen processing and presentation

15

21.17

5.49E-16

2.39E-15

31

Colorectal cancer

14

20.93

6.14E-15

2.48E-14

32

Adipocytokine signaling pathway

11

20.62

6.05E-12

1.80E-11

33

Chemokine signaling pathway

30

19.83

7.80E-30

7.35E-29

34

Prostate cancer

14

19.76

1.42E-14

5.53E-14

35

Glioma

10

19.32

1.10E-10

2.89E-10

36

Jak-STAT signaling pathway

23

18.64

1.67E-22

1.18E-21

37

Non-small cell lung cancer

8

18.61

1.13E-08

2.50E-08

38

Melanoma

10

17.69

2.71E-10

6.96E-10

39

Pathways in cancer

46

17.51

9.85E-43

2.23E-41

40

Fc epsilon RI signaling pathway

11

17.49

3.90E-11

1.05E-10

41

Chronic myeloid leukemia

10

16.75

4.74E-10

1.19E-09

42

GnRH signaling pathway

12

14.92

3.42E-11

9.43E-11

43

Leukocyte transendothelial migration

14

14.9

7.91E-13

2.48E-12

44

VEGF signaling pathway

9

14.87

1.04E-08

2.35E-08

45

Hypertrophic cardiomyopathy (HCM)

10

14.78

1.67E-09

4.10E-09

46

p53 signaling pathway

8

14.56

8.19E-08

1.75E-07

47

Endometrial cancer

6

14.49

3.65E-06

7.11E-06

48

Systemic lupus erythematosus

16

14.35

3.27E-14

1.23E-13

49

MAPK signaling pathway

30

14.01

3.15E-25

2.37E-24

50

Focal adhesion

22

13.75

1.21E-18

6.21E-18

51

Dilated cardiomyopathy

10

13.65

3.66E-09

8.44E-09

52

Type II diabetes mellitus

5

13.36

3.63E-05

6.12E-05

53

Neurotrophin signaling pathway

13

12.96

3.17E-11

8.96E-11

54

ECM-receptor interaction

8

11.96

3.85E-07

7.91E-07

55

Alzheimer's disease

16

11.89

6.32E-13

2.04E-12

56

Lysosome

11

11.81

2.86E-09

6.73E-09

57

Arginine and proline metabolism

5

11.63

7.15E-05

0.0001

58

Renal cell carcinoma

6

10.77

2.09E-05

3.63E-05

59

Long-term depression

6

10.77

2.09E-05

3.63E-05

60

Long-term potentiation

6

10.77

2.09E-05

3.63E-05

61

Proteasome

4

10.47

0.0006

0.0009

62

Progesterone-mediated oocyte maturation

7

10.22

6.00E-06

1.15E-05

63

TGF-beta signaling pathway

7

10.11

6.48E-06

1.22E-05

64

Regulation of actin cytoskeleton

16

9.3

2.69E-11

7.79E-11

65

Calcium signaling pathway

13

9.17

2.36E-09

5.67E-09

66

Wnt signaling pathway

11

9.15

4.17E-08

9.06E-08

67

Gap junction

6

8.37

8.67E-05

0.0001

68

Cell cycle

8

7.85

9.32E-06

1.70E-05

69

Oocyte meiosis

7

7.71

3.80E-05

6.31E-05

70

Axon guidance

7

6.82

8.33E-05

0.0001

71

Endocytosis

10

6.72

2.93E-06

5.81E-06

72

Metabolic pathways

26

2.96

1.12E-06

2.26E-06

  1. The table lists the number of SSKB genes associated with individual KEGG pathways. The pathways are ranked according to their Enrichment relative to the number of reference genes in the human genome based on the hypergeometric test. The raw P-values (hypergeometric test) and the multiple test-adjusted P-values are listed for each pathway.