Tuesday, 29 September 2009

Pathway identification by network pruning in the metabolic network of Escherichia coli

New paper just accepted by Bioinformatics today! Link to the pdf, abstract below:

Motivation:
All metabolic networks contain metabolites which take part in many reactions, such as ATP and NAD, known as currency metabolites. These are often removed in the study of these networks, but no consensus exists on what actually constitutes a currency metabolite, and it is also unclear how these highly connected nodes contribute to the global structure of the network.

Results:
In this paper we analyse how the Escherichia coli metabolic network responds to pruning in the form of sequential removal of metabolites with highest degree. As expected this leads to network fragmentation, but the process by which it occurs suggest modularity and long range correlations within the network. We find that the pruned networks contain longer paths than the random expectation, and that the paths that survive the pruning also exhibit a lower cost (no. of involved metabolites) compared to random paths in the full metabolic network. Finally we confirm that paths detected by pruning overlap with known metabolic pathways.
We conclude that pruning reveals functional pathways in metabolic networks, where currency metabolites may be seen as ingredients in a well-balanced soup in which main metabolic production lines are immersed.
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