Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases

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.

ISSN: 1752-0509