Using Genome-Scale Metabolic Networks for Analysis, Visualization, and Integration of Targeted Metabolomics Data

Methods Mol Biol. 2020:2104:361-386. doi: 10.1007/978-1-0716-0239-3_18.

Abstract

Interpretation of metabolomics data in the context of biological pathways is important to gain knowledge about underlying metabolic processes. In this chapter we present methods to analyze genome-scale models (GSMs) and metabolomics data together. This includes reading and mining of GSMs using the SBTab format to retrieve information on genes, reactions, and metabolites. Furthermore, the chapter showcases the generation of metabolic pathway maps using the Escher tool, which can be used for data visualization. Lastly, approaches to constrain flux balance analysis (FBA) by metabolomics data are presented.

Keywords: Analysis; Integration; Metabolic networks; Metabolomics; Visualization.

MeSH terms

  • Algorithms
  • Animals
  • Computational Biology* / methods
  • Data Analysis
  • Databases, Factual
  • Genomics* / statistics & numerical data
  • Humans
  • Metabolic Networks and Pathways*
  • Metabolomics* / statistics & numerical data
  • Models, Biological
  • Software*
  • User-Computer Interface
  • Web Browser