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Next, we enlarged the set of features by selecting the pathway
In order to evaluate the reproducibility of the pathway markers across different dataset, we performed cross-dataset experiments, where one dataset was used for selecting the pathway markers, and the other dataset was used for building the classifier based on the selected markers and evaluating its performance.
A reaction can be found by entering one or more metabolites or by selecting the pathway it is part of in one of the pathway databases.
As an example, selecting the pathway ontology in the ontology browser and typing in 'glucagon' will bring up all the terms in the ontology that contain the word glucagon.
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In this study, we selected the pathway pairs empirically, that is, those ranked in the top 10%.
Once found and selected, the Pathway database ID for the compound and/or gene symbol then becomes incorporated into the participant object that is contained in the local pathway.
We selected the pathways from the enrichment list and focused on the differentially expressed genes which distributed at the neighborhood on the pathway topology.
1. Select the pathways, knockouts and parameter sets for the desired model configuration.
Here, we selected the pathways with adjusted P-values of less than 0.01 as the significantly enriched pathways.
From DAVID analysis, we selected the pathways of Kyoto Encyclopaedia of Genes and Genomes (KEGG pathway) that include a compilation of the network of molecular interactions in cells.
Note that for each method, we selected the pathways passing either tier one or tier two criterion so that all detected pathways were included.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com