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Fig. 1 The pathway network of LPS-induced PGE2 production.
The calculations of NE and NF are heavily dependent on the completeness of the pathway network.
The network efficiency and network flux are both measures of the connectivity of the pathway network.
In the pathway network, the value of an edge (EV) represented the resistance in signal transduction.
And the binding affinity of a compound to a protein in the pathway network was assessed by molecular docking.
Actually the further downstream a node located in the pathway network, the more important it would be.
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The pathway networks were visualized using the Cytoscape package [112].
LinkinPath extracts the frequently occurred subgraphs /subnetworks from the pathway networks to discover the commonalities across the datasets (Supplementary Fig. S9).
Lastly, to identify the commonalities across multiple datasets, LinkinPath includes an algorithm to extract the frequent subnetworks from the pathway networks built in previous step.
The effective diffusivity and tortuosity of the pathways' network are also accounted for by these equivalent-circuit analyses.
Functional annotation was then assigned using the pathways, networks and out-of-network annotations found in VitisNet software http://www.sdstate.edu/aes/vitis/pathways.cfm[ 55, 93].
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