Towards metabolic networks phylogeny using Petri Net-based expansional analysis
© Lanzeni et al; licensee BioMed Central Ltd. 2007
Published: 8 May 2007
We propose a Petri Net-based method for metabolic networks profiling with respect to specific environmental conditions, based on the concept of metabolic reactions hierarchical ordering considered in . One or more metabolites are seeded in the network, then the newly synthesized compounds are iteratively integrated in the system until no new compounds could be synthesized, breeding a process of metabolic network expansion. At each step t of the network expansional process the method identifies the subset of metabolites s(t), also called "scope", that could be synthesized from the compounds available in the step t-1. The size |s(t)| of each set s(t) could be used to derive absolute and relative expansion process profiles, describing both the total number of compounds progressively incorporated and the number of new compounds synthesized in each algorithm step t.
Since natural selection acts on every structural entity of life, as it has been proven from genomic and proteomic sequences analyses, it is plausible to suppose that biological networks' structure is selected through evolution, and we prospect phylogeny approaches based on networks comparisons. In this direction the definition of a similarity metric between metabolisms based on the symmetric version of the Kullback-Leibler distance among probability distributions, applied on the profiles obtained using the method here proposed, is a promising research topic.
This article is published under license to BioMed Central Ltd.