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Table 4 Contingency table for comparing learned networks to KEGG pathways.

From: Seeded Bayesian Networks: Constructing genetic networks from microarray data

  Learned Network
Ideal (KEGG pathway) Edge in network Yes No
  Yes TP = |EL| |EI| FN = |EI| - TP
  No FP = |EL| - TP TN = [(|VI|•|VI - 1|)/2] - FN
  1. Here EL and EI represent the edges in the learned and ideal graphs, respectively, where the ideal graphs are those derived from the KEGG pathways; VI is the set of nodes (vertices) in the ideal graph.