Table 4

Contingency table for comparing learned networks to KEGG pathways.

Learned Network

Ideal (KEGG pathway)

Edge in network

Yes

No

Yes

TP = |E_L| ⋂ |E_I|

FN = |E_I| - TP

No

FP = |E_L| - TP

TN = [(|V_I|•|V_I - 1|)/2] - FN

Here E_L and E_I represent the edges in the learned and ideal graphs, respectively, where the ideal graphs are those derived from the KEGG pathways; V_I is the set of nodes (vertices) in the ideal graph.

Djebbari and Quackenbush BMC Systems Biology 2008 2:57   doi:10.1186/1752-0509-2-57