Exact(3)
Figure 2 illustrates the principle of the pattern analysis for an example pathway.
The gradient of cell phenotypes along the capsule is consistent with a cycle wherein podocytes gradually shift towards the glomerulus as shedding occurs (an example pathway is indicated by green arrows in Figure 5) [ 95, 96, 103, 104].
An example pathway and dataset are used to demonstrate the functionality of the WikiPathways app and how they can be combined and used together with other apps.
Similar(57)
Given an example, pathways in cancer, insulin signaling pathway, and other three pathways are enriched not only in obesity cluster 1 but also in T2D cluster 1, even though the gene overlap of these two clusters is very few.
We denote by f P (S) the set of atoms to which atoms in S are transferred by the pathway P. Figure 2 shows examples of f P (S) in the context of a small example pathway.
We next illustrate with an example how pathway (super) essentiality causes fragmentation of genotype networks, by demonstrating the existence of alternative essential pathways in different network components for metabolisms with 23 and 24 reactions.
Constitutive ER transcriptional regulatory activity is an example of pathway bypass: it leads to cell cycle progression and activates the anti-apoptotic protein BCL2.
Indeed, FindPath does not enumerate pathways comprising compounds (bootstraps) that are consumed before being produced unless they were added as supplement in the growth medium (cf. in Additional file 3 an example of pathway enumeration with FindPath using bootstrap compounds).
The well-studied PI3K signaling pathway is an example of a conserved pathway involved in chemotaxis that permits polarization of the cell and is important for cell speed and directionality (Parent, 2004).
In addition, amino acid metabolism is an example of a pathway with multiple routes to yield similar compounds from different routes, characterized for alternative pathways.
Figure 2 shows an example of a pathway analysis workflow with KEGGscape.
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