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Using Pathway Covering to Explore Connections among Metabolites

Bioinformatics Research Group, SRI, International, Menlo Park, CA 94025, USA
Biocomplexity Sciences, SRI International, Menlo Park, CA 94025, USA
Author to whom correspondence should be addressed.
Metabolites 2019, 9(5), 88;
Received: 16 March 2019 / Revised: 24 April 2019 / Accepted: 26 April 2019 / Published: 2 May 2019
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Interpreting 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
Keywords: metabolite sets; set theory; optimization; pathways; BioCyc metabolite sets; set theory; optimization; pathways; BioCyc

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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.

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