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Escher-Trace: a web application for pathway-based visualization of stable isotope tracing data.

Avi Kumar1, Jack Mitchener1, Zachary A King1

  • 1Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.

BMC Bioinformatics
|July 12, 2020
PubMed
Summary

Escher-Trace is a new web-based software that simplifies stable isotope tracing data analysis. It integrates data with metabolic networks, enhancing biological interpretation for researchers.

Keywords:
EscherMetabolismStable isotope tracingVisualizationWeb application

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Area of Science:

  • Metabolic engineering
  • Systems biology
  • Biotechnology

Background:

  • Stable isotope tracing is crucial for studying biological metabolism.
  • Current analysis methods are fragmented, requiring multiple software packages and lacking pathway integration.
  • Interpreting complex metabolic tracing data necessitates understanding its biological context.

Purpose of the Study:

  • To develop a unified software solution for analyzing and visualizing stable isotope tracing data.
  • To integrate tracing data with metabolic pathway information for enhanced biological interpretation.

Main Methods:

  • Developed Escher-Trace, a standalone, web-based software.
  • Enabled users to upload and baseline correct mass spectrometry (MS) tracing data.
  • Incorporated natural isotope abundance correction.
  • Facilitated the generation of publication-quality graphs of metabolite labeling.
  • Allowed data visualization within annotated or custom metabolic networks.

Main Results:

  • Escher-Trace provides a user-friendly platform for analyzing stable isotope tracing data.
  • The software enables the integration of tracing data with metabolic pathway architecture.
  • Publication-quality graphs and visualizations of metabolite labeling are generated.
  • A detailed walk-through for incorporating 13C metabolic tracing data is provided.

Conclusions:

  • Escher-Trace is an open-source software tool for the analysis and interpretation of stable isotope tracing data.
  • The platform enhances the understanding of metabolic processes by integrating tracing data with pathway information.
  • Escher-Trace is accessible at https://escher-trace.github.io/