Table 4

Performance of our method to predict drug-CRGs under different thresholds
Threshold of degree* Threshold of betweenness centrality The proposed method Method based on gene expression
Number of identified CCRGs enrichement significance Number of identified CCRGs# enrichement significance
0.01 0.01 6 1.20E-08 5 5.34E-06
0.02 0.02 8 0.00 6 1.05E-05
0.03 0.03 10 0.00 7 5.76E-06
0.04 0.04 11 0.00 7 2.87E-05
0.05 0.05 11 0.00 7 1.20E-04
0.06 0.06 11 0.00 8 4.56E-05
0.07 0.07 13 0.00 8 1.17E-04
0.08 0.08 13 0.00 8 2.61E-04
0.09 0.09 13 7.46E-08 8 5.47E-04
0.1 0.1 13 2.01E-08 8 8.87E-04
0.11 0.11 13 1.08E-08 9 3.05E-04
0.12 0.12 14 6.10E-08 9 5.71E-04
0.13 0.13 14 0.00 11 5.07E-05
0.14 0.14 14 3.60E-07 11 7.91E-05
0.15 0.15 14 7.63E-07 11 1.30E-04
0.16 0.16 14 1.79E-06 11 2.40E-04
0.17 0.17 14 2.80E-06 11 3.26E-04
0.18 0.18 14 5.26E-06 11 5.14E-04
0.19 0.19 14 7.77E-06 11 6.89E-04
0.2 0.2 15 3.25E-06 11 1.13E-03

*Degree threshold is set to one percentile (0.01) of degree for all the genes in HPRD. And 0.02 represents that we set the degree threshold as two percentile of degree for all the genes in HPRD. Betweenness centrality threshold is set in the same way as degree threshold.

#In order to ensure the comparability of our method and the method based on correlation of gene expression and drug activity, we kept the number of drug-CRGs obtained by both methods equal with each other.

Chen et al.

Chen et al. BMC Medical Genomics 2012 5:43   doi:10.1186/1755-8794-5-43

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