Table 3.

Evaluating the resulting subnetworks based on gene level/gene-set level agreement

Data	GGI			PPI
	GNFS-greedy [14]	GSNFS-GS	GSNFS-PN	GNFS-greedy [14]	GSNFS-GS	GSNFS-PN
Gene level
Lung1*2	0.099	0.138	0.118	0.186	0.140	0.145
Lung1*3	0.023	0.004	0.068	0.047	0.087	0.085
Lung1*4	0.047	0.084	0.094	0.1	0.108	0.127
Lung2*3	0.043	0.019	0.096	0.081	0.104	0.107
Lung2*4	0.091	0.105	0.121	0.087	0.1	0.076
Lung3*4	0.037	0	0.084	0.143	0.076	0.104
Gene-set level
Lung1*2	0.2	0.319	0.453	0.23	0.23	0.316
Lung1*3	0.058	0.0115	0.272	0	0.056	0.16
Lung1*4	0.125	0.103	0.308	0.08	0.179	0.366
Lung2*3	0.037	0.015	0.321	0.059	0.125	0.175
Lung2*4	0.083	0.219	0.34	0	0.174	0.167
Lung3*4	0.095	0	0.2375	0.111	0.148	0.2

The gene/gene-set level agreement is a ratio between the number of common genes/gene-sets found in two datasets and the total number of genes/gene-sets identified from the two datasets. The gene/gene-set level agreements were calculated for different searching strategies and presented above