back icon
close icon

Capture phrases in quotes for more specific queries (e.g. "rocket ship" or "Fred Lynn")

Article  May 2, 2019

Using pathway covering to explore connections among metabolites

SRI Authors Paul O’Maille, Mario Latendresse, Peter Karp



Midford, P.E., Latendresse, M., O’Maille, P.E. & Karp, P.D. Using pathway covering to explore connections among metabolites. Metabolites 9 (2019).


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.

How can we help?

    Once you hit send…

    We’ll match your inquiry to the person who can best help you. Expect a response within 48 hours.

    Our Privacy Policy