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Issue 11, 2011
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An extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks

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Abstract

The bioreaction database established by Ma and Zeng (Bioinformatics, 2003, 19, 270–277) for in silico reconstruction of genome-scale metabolic networks has been widely used. Based on more recent information in the reference databases KEGG LIGAND and Brenda, we upgrade the bioreaction database in this work by almost doubling the number of reactions from 3565 to 6851. Over 70% of the reactions have been manually updated/revised in terms of reversibility, reactant pairs, currency metabolites and error correction. For the first time, 41 spontaneous sugar mutarotation reactions are introduced into the biochemical database. The upgrade significantly improves the reconstruction of genome scale metabolic networks. Many gaps or missing biochemical links can be recovered, as exemplified with three model organisms Homo sapiens, Aspergillus niger, and Escherichia coli. The topological parameters of the constructed networks were also largely affected, however, the overall network structure remains scale-free. Furthermore, we consider the problem of computing biologically feasible shortest paths in reconstructed metabolic networks. We show that these paths are hard to compute and present solutions to find such paths in networks of small and medium size.

Graphical abstract: An extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks

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Publication details

The article was received on 26 Jan 2011, accepted on 02 Aug 2011 and first published on 27 Sep 2011


Article type: Paper
DOI: 10.1039/C1IB00008J
Citation: Integr. Biol., 2011,3, 1071-1086
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    An extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks

    M. Stelzer, J. Sun, T. Kamphans, S. P. Fekete and A. Zeng, Integr. Biol., 2011, 3, 1071
    DOI: 10.1039/C1IB00008J

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