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Using Pathway Covering to Explore Connections among Metabolites

1
Bioinformatics Research Group, SRI, International, Menlo Park, CA 94025, USA
2
Biocomplexity Sciences, SRI International, Menlo Park, CA 94025, USA
*
Author to whom correspondence should be addressed.
Metabolites 2019, 9(5), 88; https://doi.org/10.3390/metabo9050088
Received: 16 March 2019 / Revised: 24 April 2019 / Accepted: 26 April 2019 / Published: 2 May 2019
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Abstract

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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