MetExplore - Metabolic network content

Metabolic network reconstruction
Biosources
KEGG
BioCyc
SBML
Goal

Where metabolic networks come from (reconstruction) ? How they are stored ? How they can be mined using MetExplore ?

  • Use metabolic networks knowing how they are built and what is there content
  • Browse BioSource content in MetExplore
Prerequisites

General knowledge on metabolism.

Introduction

Metabolic fingerprints (list of metabolites of interest) identified using metabolomics can be put back in a biochemical context using metabolic networks. Metabolic networks aim at gathering all metabolic reactions an organism can perform. This section is dedicated to introduce the basic concepts undelrying genome scale metabolic network reconstruction. It will also provides some pointers towards repositories where metabolic networks can be found and used. Finally the course will present how metabolic network content can be browsed using MetExplore.

Summary

The slideshow will present concept and databases related to genome scale metabolic networks. Then it will give a quick overview of these networks in MetExplore.

Contents
Conclusion

This course allowed to understand how network are reconstructed and how they can be accessed. The course also introduced the concept of Biosource and how it can be browsed in MetExplore web server.

References
  • www.metexplore.fr  
  • https://www.genome.jp/kegg/
  • https://biocyc.org/
  • http://sbml.org/Main_Page
  • Thiele,I. and Palsson,B.Ø. (2010) A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat. Protoc., 5, 93–121.
  • Kanehisa,M., Furumichi,M., Tanabe,M., Sato,Y. and Morishima,K. (2017) KEGG: New perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res., 45, D353–D361.
  • Caspi,R., Billington,R., Ferrer,L., Foerster,H., Fulcher,C.A., Keseler,I.M., Kothari,A., Krummenacker,M., Latendresse,M., Mueller,L.A., et al. (2016) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res., 44, D471-80.