Table 2 |
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|
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 |
|
|
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|
* 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 |
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