Monday, 22 March 2010

Predicting Novel Metabolic Pathways in Genome-Scale Networks.

Stefan Schuster

Need systematic methods.

Decompose network into pathways. Need stoichiometries and reversibility.
Elementary modes are minimum sets of enzymes that can operate at steady state. Enzymes are weigted by their flux. Clipping of complete space for irreversibility to create a pyramid in high dimensions.

A connected route is not enough to infer a process occurs at steady state you need to do elementary mode analysis. Bioinformatics Schuster paper and discussion with other group. Other group defending graph theoretical models.

All metabolites that are involved in more than 4 reactions are specified as external metabolites.

Genome Research 19 2009 1872-1883 can work on sub-systems of the complete genome model so long as you perform a consistency check.

Modularity reduces the combinatorial problem of checking networks for all elementary modes. Not consistent if in the complete model the reagants used in the synthesis of a product are generated by the subsequent reactions of the product.

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