• Skip to primary navigation
  • Skip to main content
SRI InternationalSRI mobile logo

SRI International

SRI International - American Nonprofit Research Institute

  • About
    • Blog
    • Press room
  • Expertise
    • Advanced imaging systems
    • Artificial intelligence
    • Biomedical R&D services
    • Biomedical sciences
    • Computer vision
    • Cyber & formal methods
    • Education and learning
    • Innovation strategy and policy
    • National security
    • Ocean & space
    • Quantum
    • QED-C
    • Robotics, sensors & devices
    • Speech & natural language
    • Video test & measurement
  • Ventures
  • NSIC
  • Careers
  • Contact
  • 日本支社
Show Search
Hide Search
Biomedical sciences publications May 2, 2019 Article

Using pathway covering to explore connections among metabolites

Paul O’Maille, Mario Latendresse, Peter Karp May 2, 2019

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

Citation

Copy to clipboard


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

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.

Share this

Facebooktwitterlinkedinmail

Biomedical sciences publications, Information & computer science publications, Publication Article

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.

Career call to action image

Make your own mark.

Search jobs
Our work

Case studies

Publications

Timeline of innovation

Areas of expertise

Blog

Institute

Leadership

Press room

Media inquiries

Compliance

Privacy policy

Careers

Job listings

Contact

SRI Ventures

Our locations

Headquarters

333 Ravenswood Ave
Menlo Park, CA 94025 USA

+1 (650) 859-2000

Subscribe to our newsletter

日本支社

SRI International

  • Contact us
  • Privacy Policy
  • Cookies
  • DMCA
  • Copyright © 2022 SRI International