ReporterPathways Web Tool provides tools to determine significantly perturbed metabolic pathways, called reporter pathways, by mapping transcriptome data on organism-specific genome-scale metabolic networks. The Tool is a web implementation of the methods introduced in detail in Çakır et al., (2015). The methods cover the classic reaction-centric reporter pathway analysis approach (RPAr) and the newly introduced metabolite-centric reporter pathway analysis approach (RPAm).
Comparison of reaction-centric and metabolite-centric reporter pathway analysis approaches The change in gene activities corresponding to reactions R4, R5, R6 and R7 are not counted in RPAr to calculate the pathway activity since they are categorized under other pathways. On the other hand, they are considered in the metabolite-centric RPAm since all reactions producing or consuming the metabolites of the pathway are taken into account. (Mi: metabolites, Ri: reactions, gi: genes, pi: p-values)
ReporterPathways Web Tool allows the user to create an account, thus it will be easier for the user to maintain their results history. The code was written in R, and the web itself has Python-Django as the backend and CSS Bootstrap for template.
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