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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.
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.
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.
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.
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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.
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.
For example, pathways 175 and 73 are predicted to be a pair of parallel pathways.
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