SANTA: Quantifying the Functional Content of Molecular Networks
Figure 3
Application of Knetto simulated networks.
Scale-free networks containing clusters of high-weight nodes of various strengths were generated. The smaller the distance cutoff used to generate the cluster, the greater the strength of the clustering. (A) 1000 trials were completed for each distance cutoff. As expected, the most significant clustering was measured by the Knet-function when smaller distance cutoffs were used. (B) Q-Q plot of the p-values observed in the simulation study trials in which no distance cutoff was used and the p-values expected under the uniform distribution. The high-weight nodes were distributed homogeneously when no distance cutoff was used. The observed p-values deviate little from the expected p-values, demonstrating that the Knet-function does not detect clustering when clustering is not present.