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- Title
Using Pathway Covering to Explore Connections among Metabolites.
- Authors
Midford, Peter E.; Latendresse, Mario; O'Maille, Paul E.; Karp, Peter D.
- 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.
- Subjects
METABOLITES; SOFTWARE development tools; INVESTIGATIONAL therapies; DISEASE progression; THERAPEUTICS; TRANSPORTATION software
- Publication
Metabolites (2218-1989), 2019, Vol 9, Issue 5, p88
- ISSN
2218-1989
- Publication type
Article
- DOI
10.3390/metabo9050088