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Table 3 Evaluating the resulting subnetworks based on gene level/gene-set level agreement

From: GSNFS: Gene subnetwork biomarker identification of lung cancer expression data

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
  1. 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