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Here, the co-expression value of a pair of pathway was presented by the arithmetic average of Jaccard coefficient and overlap coefficient (see Methods section for details).
In a biological point of view, a pair of pathway can interact with each other if they are expressed at the same time and in the same place, e.g. tissue.
Similar(58)
But, the pathway crosstalk, as a pair of pathways, also plays important roles in the change of phenotypes [ 25].
Thus, an inter-species alignment of a pair of pathways is considered biochemically validated if the alignment maps reaction subsets classified under the same FGC category.
This approach assumes that a pathway edge exists if significantly more protein-protein (P-P) interactions are detected between a pair of pathways than expected by chance.
Our predicted pathway pairs represent the redundancy mechanism between a pair of pathways in which proteins can compensate for each other to perform in the same or functionally related biological process.
Both studies were based on the assumption that a pair of pathways is likely to interact when a higher number of protein-protein interactions are found between them than would be expected by chance.
From both AS metrics, and given a pair of pathways i and j, the functional association strength between these two pathways (bASpij or mASpij) was computed as the sum of the functional association scores of all the gene pairs which can be established between these pathways.
We introduced two measurements to computationally indicate the overlap of a pair of pathways: the Jaccard Coefficient JC = A ∩ B A ∪ B and the Overlap Coefficient OC = A ∩ B min (A, B ), where A and B denote the number of candidate genes in the two pathways, respectively.
Consider a model consisting of a pair of protein pathways where each pathway serves as a redundant backup for the other.
Motivation: Given a pair of metabolic pathways, an alignment of the pathways corresponds to a mapping between similar substructures of the pair.
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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