Using Pathway Covering to Explore Connections among Metabolites

Metabolites

PaulE. O’Maille¹  Mario Latendresse²  PeterD. Karp²  PeterE. Midford² 

[1] Biocomplexity Sciences, SRI International, Menlo Park, CA 94025, USA;Bioinformatics Research Group, SRI, International, Menlo Park, CA 94025, USA;

关键词: metabolite sets;    set theory;    optimization;    pathways;    BioCyc;   

DOI  :  10.3390/metabo9050088

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown