Table 3.
Q-values of pathways detected by GIENA for three breast cancer datasets
| Pathways | Cooperation | Competition | Redundancy | Dependency | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| |
Dataset 1 |
Dataset 2 |
Dataset 3 |
Dataset 1 |
Dataset 2 |
Dataset 3 |
Dataset 1 |
Dataset 2 |
Dataset 3 |
Dataset 1 |
Dataset 2 |
Dataset 3 |
|
P27 |
0.027 |
0.021 |
0.0073 |
0.019 |
0.025 |
0.016 |
0.023 |
0.038 |
0.019 |
0.014 |
0.010 |
0.0062 |
|
FBW7 |
0.018 |
0.021 |
0.0071 |
0.019 |
0.028 |
0.016 |
0.021 |
0.030 |
0.019 |
0.0062 |
0.020 |
0.010 |
| PTC1 |
0.018 |
0.0073 |
0.010 |
<0.0001 |
0.0013 |
0.014 |
0.012 |
0.013 |
0.019 |
0.0097 |
0.015 |
0.025 |
| Cell cycle |
0.018 |
0.018 |
0.010 |
0.0082 |
0.021 |
0.014 |
0.021 |
0.032 |
0.019 |
0.0043 |
0.0020 |
0.017 |
| SRCRPTP |
0.0021 |
<0.0001 |
0.0063 |
0.0022 |
0.0074 |
0.016 |
0.0018 |
0.002 |
0.0036 |
<0.0001 |
0.0010 |
0.012 |
| G2 &M phase |
0.0095 |
0.0056 |
0.010 |
0.0015 |
0.0033 |
0.014 |
0.014 |
0.020 |
0.019 |
0.0017 |
0.0010 |
0.017 |
| Cyclin |
0.018 |
0.015 |
0.010 |
0.0017 |
0.021 |
0.016 |
0.021 |
0.029 |
0.018 |
0.0021 |
0.0010 |
0.010 |
| RB |
0.0095 |
0.0078 |
0.0071 |
0.0081 |
0.0092 |
0.016 |
0.014 |
0.020 |
0.018 |
0.0017 |
0.0023 |
0.017 |
| G2 |
0.0021 |
0.0056 |
0.010 |
0.0082 |
0.016 |
0.016 |
0.0018 |
0.013 |
0.019 |
0.0014 |
0.0023 |
0.020 |
| SKP2E2F |
0.015 |
0.018 |
0.0071 |
0.019 |
0.029 |
0.016 |
0.019 |
0.025 |
0.018 |
0.0043 |
0.015 |
0.0086 |
| CDC25 | 0.0035 | 0.0033 | 0.0073 | 0.0082 | 0.016 | 0.016 | 0.0093 | 0.013 | 0.018 | <0.0001 | 0.0010 | 0.017 |
q-value < 0.01 is considered as significant, and q-values for pathways with significant q-values for at least two datasets are highlighted in bold.
Two pathways detected by GIENA only are in italics.
Dataset 1: GSE7390; Dataset 2: GSE19615; Dataset 3: GSE26639.
Only pathways detected by at least two datasets listed.
Both P27 and FBW7 pathways are in top 25 pathways in normal GSA results in all three datasets.