Using Pathway Covering to Explore Connections among Metabolites
AbstractInterpreting changes in metabolite abundance in response to experimental treatments or disease states remains a major challenge in metabolomics. Pathway Covering is a new algorithm that takes a list of metabolites (compounds) and determines a minimum-cost set of metabolic pathways in an organism that includes (covers) all the metabolites in the list. We used five functions for assigning costs to pathways, including assigning a constant for all pathways, which yields a solution with the smallest pathway count; two methods that penalize large pathways; one that prefers pathways based on the pathway’s assigned function, and one that loosely corresponds to metabolic flux. The pathway covering set computed by the algorithm can be displayed as a multi-pathway diagram (“pathway collage”) that highlights the covered metabolites. We investigated the pathway covering algorithm by using several datasets from the Metabolomics Workbench. The algorithm is best applied to a list of metabolites with significant statistics and fold-changes with a specified direction of change for each metabolite. The pathway covering algorithm is now available within the Pathway Tools software and BioCyc website. View Full-Text
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Midford, P.E.; Latendresse, M.; O’Maille, P.E.; Karp, P.D. Using Pathway Covering to Explore Connections among Metabolites. Metabolites 2019, 9, 88.
Midford PE, Latendresse M, O’Maille PE, Karp PD. Using Pathway Covering to Explore Connections among Metabolites. Metabolites. 2019; 9(5):88.Chicago/Turabian Style
Midford, Peter E.; Latendresse, Mario; O’Maille, Paul E.; Karp, Peter D. 2019. "Using Pathway Covering to Explore Connections among Metabolites." Metabolites 9, no. 5: 88.
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