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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.