Journal
BIOESSAYS
Volume 32, Issue 3, Pages 246-256Publisher
WILEY
DOI: 10.1002/bies.200900145
Keywords
bipartite networks; hierarchical modularity; metabolic networks; scale-free; small-world
Categories
Funding
- EU [NEST-043241]
- James S. McDonnell Foundation
- Santa Fe Institute
- Spanish Ministry of Science and Innovation [SAF 2008-02522]
- Fundacion Ramon Areces [P07-CVI-02999]
- Andalusian Government [BIO-267]
- ICREA Funding Source: Custom
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The search for a systems-level picture of metabolism as a web of molecular interactions provides a paradigmatic example of how the methods used to characterize a system can bias the interpretation of its functional meaning. Metabolic maps have been analyzed using novel techniques from network theory, revealing some non-trivial, functionally relevant properties. These include a small-world structure and hierarchical modularity. However, as discussed here, some of these properties might actually result from an inappropriate way of defining network interactions. Starting from the so-called bipartite organization of metabolism, where the two meaningful subsets (reactions and metabolites) are considered, most current works use only one of the subsets by means of so-called graph projections. Unfortunately, projected graphs often ignore relevant biological and chemical constraints, thus leading to statistical artifacts. Some of these drawbacks and alternative approaches need to be properly addressed.
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