Therefore, we decided to use the rat functional linkage network predicted by the STRING system [18].
At the heart of the methodology are the concept of Linked Processes and the resultant network of biological processes, the Process Linkage Network (PLN).
Given an intracellular interaction network for an organism and Gene Ontology annotations for the genes in those networks, Dotan-Cohen et al. compute what they term a Biological Process Linkage Network (BPLN).
We propose a novel approach called "Contextual Biological Process Linkage Network" (CBPLN) that focuses on computing which processes in the cell are perturbed in a particular context and how these processes are linked to each other.
At the heart of the methodology described in the paper are the concept of Linked Processes and the resultant new network of biological processes, the Process Linkage Network (PLN), whose nodes correspond to biological process terms in the Gene Ontology (GO) database.
Comparison of the functional linkage network with previously published networks.
The underlying functional linkage network is shown in Figure 4.
Yong, et al. constructed a global pathway crosstalk network and linkage network for yeast [ 5].
The functional linkage network was generated using STRING 9.0 database [ 44].
