Table 2

PANTHER analysis of differentially expressed genes by pathway.

Pathway

number of genes in reference list

number of regulated genes

Expected number of genes

P-value*


Pathways that are overrepresented taking up-regulated genes into account

Integrin signaling pathway

185

19

3.48

4.78E-09

WNT signaling pathway

348

22

6.55

1.27E-06

Angiogenesis

193

12

3.63

3.76E-04

Cadherin signaling pathway

167

11

3.14

4.07E-04

Alzheimer disease-presenilin pathway

124

9

2.33

6.84E-04

Pathways that are overrepresented taking downregulated genes into account

B cell activation

87

21

3.01

1.03E-11

p53 pathway

127

18

4.39

8.32E-07

Inflammation mediated by chemokine and cytokine signaling pathway

298

29

10.30

1.12E-06

Blood coagulation

55

10

1.90

2.96E-05

p53 pathway feedback loops 2

51

9

1.76

9.15E-05

Parkinson disease

106

13

3.66

1.13E-04

Cell cycle

24

6

0.83

2.21E-04

Integrin signaling pathway

185

17

6.39

3.38E-04

De novo pyrimidine deoxyribonucleotide biosynthesis

23

5

0.79

1.36E-03

DNA replication

25

5

0.86

1.95E-03

Ras Pathway

80

9

2.76

2.20E-03

Apoptosis signaling pathway

141

12

4.87

4.37E-03

T cell activation

142

12

4.91

4.61E-03

JAK/STAT signaling pathway

20

4

0.69

5.48E-03

Angiogenesis

193

14

6.67

8.51E-03

Pathways that are overrepresented taking up- and down-regulated genes into account

Integrin signaling pathway

185

36

9.87

7.87E-09

B cell activation

87

24

4.64

7.10E-09

Inflammation mediated by chemokine and cytokine signaling pathway

298

41

15.90

2.42E-06

p53 pathway

127

21

6.78

1.79E-04

Angiogenesis

193

26

10.30

4.45E-04

Blood coagulation

55

12

2.93

8.00E-04

p53 pathway feedback loops 2

51

9

2.72

2.42E-02

Cell cycle

24

6

1.28

2.19E-02

WNT signaling pathway

348

31

18.57

4.57E-02

Axon guidance mediated by netrin

29

6

1.55

4.36E-02

Parkinson disease

106

13

5.66

4.22E-02


* P-values are obtained by the binomial test; only P-values that fulfilled an additional false discovery rate test are shown.

Lodewyckx et al. Arthritis Research & Therapy 2012 14:R16   doi:10.1186/ar3695

Open Data