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An exemplary comparison between a subnetwork of metabolic pathways and related system of stable correlations is shown on Fig. 4. It is important to note, that correlation between amino acids might be a result not only of their common biosynthetic pathways but also of their coordinated outflow for protein synthesis or conversely, a result of amino acids release as a result of protein degradation.
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There are 34 genes shared by the two N-C subnetworks, including one common hub - APC. FYN, a hub discovered in GSE14323 N-C subnetwork, is also a hub in E-A subnetwork of GSE6467.
Triad represents a subnetwork of three directly connected nodes.
In the previous subsection we showed a subnetwork of the transcriptional regulatory network that was obtained by searching shortest paths between all periodic genes.
A metabolic pathway is a subnetwork of the metabolic network.
Step six: Construction a subnetwork consisting of all shortest paths between the candidate genes from the giant network.
Originally, a subnetwork consisting of CoreMitoP proteins was reconstructed from global Arabidopsis PIN.
These interactions form a distinct subnetwork of highly conserved interactions.
The parameter α balances between two types of solutions: (1) a subnetwork with minimum number of labels (α = 1), which is equivalent to the union of independent Steiner trees for each of the conditions, and (2) a subnetwork with minimum number of edges (α = 0), which is simply a Steiner tree spanning the terminals in the union of all conditions.
The connectivity of a subnetwork is the ratio between the number of links from the subnetwork to the rest of the network and the number of links within the subnetwork [ 36].
By mapping differentially expressed genes to the subnetwork described above, we finally obtained a subnetwork that consists of 127 genes except seed genes and 259 interactions.
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CEO of Professional Science Editing for Scientists @ prosciediting.com