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In all cases, pathways or enzyme classifications for prokaryotic or plant-specific genes were absent in the KAAS results.
For example, a pathway was removed if it did not contain any enzymes that were unique to the pathway and there was no experimental evidence for the pathway existence in the Leishmania spp. In some cases, pathways were deleted and replaced with Leishmania-specific pathways.
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In such cases, pathway nodes should not be linked to any node via interactions.
In such cases, pathway analysis provides important organizational information on the potential action of sets of genes.
Thus TCS pathway structure is often more elaborate than the basic two-component paradigm, and in such cases pathway structure cannot usually be inferred from TCS gene structure.
In some cases, pathway map nodes are presented to indicate that some nodes and edges are a part of another pathway.
In all cases, pathway expression started with PAL except for E. coli in which TAL was the first enzyme introduced [ 70].
> The succession and clustering of interventions that we see in at least four cases (pathway b) does not appear to be an isolated occurrence.
Specifically, we used standard hierarchical clustering and clustering with support trees [34]: in the latter case pathways and samples were bootstrapped over 100 and 1000 iterations.
These are the branching case pathways (present or absent) and structured clinical reasoning feedback (present or absent).
A Bayesian network is a graphical model representing probabilistic relationships between different factors (in our case pathways) [ 45].
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