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The above simulation has relevance for the case of pathways which are costimulated, and which have common downstream targets.
In the case of pathways corresponding to overall reaction [4], five of the distinct pathway reactions were classified as blocked.
In the case of pathways 2 7, SLN biopsy is performed using either blue dye, 99mTc, or both, in order to identify the SLN.
Thus, in the case of pathways with weak signals from the annotation number point of view, MPINet can also identify these by considering the additional global network structure.
Given that KEGG pathways contain collections of genes involved in extensive biochemical processes, we further proceed to work with KEGG modules, following a similar rationale to the one applied in the case of pathways.
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In the case of pathway member proteins, basic information also includes pathway memberships and topological properties.
This result is illustrated for the case of pathway enumeration between chorismate and tyrosine in E. coli for different heights h using a reaction representation at the level of the 3rd digit in the EC number classification.
The comparison of metabolic profiles of Sodalis glossinidius and tsetse fly primary endosymbiont Wiglesworthia glossinidia based on their whole gene and pseudogene repertoires revealed a novel case of pathway inactivation, the arginine biosynthesis, in Sodalis glossinidius together with a possible case of metabolic complementation with Wigglesworthia glossinidia for thiamine biosynthesis.
There are cases of pathways with similar names, which do not get unified into the same SuperPath.
When constructing a network only from the lineage-specific pathways, one can observe that, unlike the case of universal pathways, lineage-specific pathways do not form a single-component network.
The previous example illustrates the benefit of multi-seed pathway inference in the case of linear pathways.
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