The phenotypes of multiple C3 C4 species were used to identify pathways compatible with individual species (e.g., Alternanthera ficoides [red nodes] and Parthenium hysterophorus [blue nodes]), and pathways compatible with the phenotypes of multiple species (purple nodes).
Specifically, we hypothesize that fixed changes in gene product concentration levels - resulting from the changes in gene transcription levels - act as small adjustments while we assume that the number of pathway nodes and the pathway structure remain unchanged.
In detail node and pathway activity moves along the following steps after transient MET receptor signalling: (i) the first and necessary input into the network towards migration is the stimulation with HGF, which immediately and specifically activates the MET receptor.
The simplified causal BN from MetS to NAFLD retained 17 nodes and 98 pathways (shown in figure 5).
After that, some most relevant regulating networks were considered, which included the nodes and relevant pathways of dioscin.
Then we plotted the pathway as nodes and linked two pathways by an edge if the two pathways have overlapping genes.
A further evaluation performed with Ingenuity Pathway analysis revealed that these genes are nodes of networks and pathways that are involved in the modulation of Ca2+ homeostasis as well as in the regulation of glutamatergic transmission and synaptic plasticity.
We then construct a molecular interaction network, where the nodes are genes and pathways, and the edges are added in the following way: 1) Text-mined results: all interactions detected by PWTEES are added to the edge set.
This analysis shows that after the removing of orphan nodes, the genes (and pathways) identified to be significantly induced by L. major in macrophages derived from susceptible mice, mostly unique to BALB/c appeared to be interconnected except for the p53 signaling pathway.
PathExpand (Glaab et al., 2010a) maps the input pathway/process onto the human protein protein interaction network and extends it with proteins that (1) are strongly associated with the pathway nodes; and (2) increase the pathway compactness by connecting its disconnected members.
The commonly used node-and-edge description of pathways, where nodes represent proteins and edges the interactions between them, are useful, but do not provide structural interaction detail [ 33, 34].
