We used the P-MAP program [ 27] with E-value ≤ 10-6, in conjunction with BLAST [ 28] with E-value ≤ 10-20, to map template networks to WH8102.
Figure 2(a) shows the template network that was used to obtain the data that were used in lieu of experimental data.
Given that kinetic parameters are typically unknown and need to be estimated, there is a strong case to be made for the fact that no single network that can be obtained from a completely automated reverse engineering approach can identify the template network that gave rise to the observed phenotype in the first place.
By using P-MAP [ 27] and BLAST [ 28], we were able to map the genes from the five (partial) template networks outlined above to 28 genes in WH8102 (Additional files 1, 2, 3, 4 and 5), providing the components of our initial osmoregulation network model of WH8102.
To load the template network into Cytoscape, use a web browser on a workstation having at least 6GB RAM.
The CNTs backbone serves as a shape template and conducting network to facilitate electron and lithium ion transport, while the carbon coating acts as a buffering layer to maintain the structural integrity of the electrode upon cycling.
Figure 2 Pathway GeneSWAPPER (PGS) can be utilized not only to project a new species network but also to enrich the existing template network.
Although this is not a conclusive proof of the fact that the behavior observed in the previous section is not completely due to the suboptimality of the template network, it does show that regardless of the type of network, the many-to-one phenotype-genotype mapping can lead to an indeterminacy of the reverse engineering problem.
Despite the wide range of wiring patterns and interaction types (PTM, auto regulation, activation and repression), the protein profiles for all these different networks are remarkably similar to that of the template network shown in Figure 2(b).
Interestingly, both the optimized networks had a distance function value of 0; that is, the protein levels at the sampling points were identical to those produced by the template network.
