How to identify, within a genome scale metabolic network, a subnetwork (subset of all reactions) connecting metabolites belonging to a metabolic fingerprint ?
At the end of the course, you will be able to :
- understand how a network is turned into a graph model.
- understand path search in metabolic networks and its limits.
- knows how to extract a metabolic sub-network.
Knowing what is a metabolic network.
Metabolic pathways provide a fragmented view of metabolism. By using networks it is possible to get an holistic perspective of the metabolic context of metabolomics data. Nevertheless it requires computational solutions (algorithms) to extra parts of this network (subnetwork) which are likely to be modulated and thus connected to a metabolic fingerprint.
The slideshow will explain how the network is turned into a graph. Then it will introduce various options to compute metabolic paths between metabolites. Finally it will show how these paths can be merged to create a subnetwork.
Metabolic network based analysis allow to extract a subnetwork which may span several metabolic networks. It is important to know the limitations of the various algorithms available.
- Faust,K. and van Helden,J. (2012) Predicting metabolic pathways by sub-network extraction. Methods Mol. Biol., 804, 107–30. https://doi.org/10.1007/978-1-61779-361-5_7
- Frainay,C. and Jourdan,F. (2017) Computational methods to identify metabolic sub-networks based on metabolomic profiles. Brief. Bioinform., 18, 43–56. https://doi.org/10.1093/bib/bbv115
- Lacroix,V., Cottret,L., Thébault,P. and Sagot,M.-F. (2008) An introduction to metabolic networks and their structural analysis. IEEE/ACM Trans. Comput. Biol. Bioinform., 5, 594–617. https://doi.org/10.1109/TCBB.2008.79