Open Access Highly Accessed Methodology article

Integration of metabolic databases for the reconstruction of genome-scale metabolic networks

Karin Radrich12, Yoshimasa Tsuruoka34, Paul Dobson5, Albert Gevorgyan67, Neil Swainston8, Gino Baart9 and Jean-Marc Schwartz1*

Author Affiliations

1 Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK

2 Helmholtz-Zentrum München, Technische Universität München, 80333 München, Germany

3 National Centre for Text Mining, University of Manchester, Manchester M1 7DN, UK

4 Japan Advanced Institute of Science and Technology, Nomi, Ishikawa 923-1292, Japan

5 School of Chemistry, University of Manchester, Manchester M1 7DN, UK

6 Cell Systems Modelling Group, School of Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK

7 Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK

8 Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester M1 7DN, UK

9 VIB Department of Plant Systems Biology/Department of Biology, Ghent University, 9052 Gent, Belgium

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BMC Systems Biology 2010, 4:114  doi:10.1186/1752-0509-4-114

Published: 16 August 2010

Additional files

Additional file 1:

Compound and reaction data of the core (yellow) metabolic network. The first sheet contains the list of compounds and the second sheet the list of reactions. Each compound is identified by a local identifier consisting of "Ath_C" followed by a four-digit number, its Kegg identifier and AraCyc name. Each reaction is identified by a local identifier consisting of "Ath_R" followed by a four-digit number, its Kegg identifier and AraCyc name. The stoichiometry column describes the reaction using local compound identifier. Substrates and products are separated by the equal ("=") sign. The stoichiometry is always explicitly written even when it is one. The enzyme column lists the enzymes catalysing each reaction by their EC number.

Format: XLS Size: 264KB Download file

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Additional file 2:

Compound and reaction data of the intermediate (green) metabolic network. The first sheet contains the list of compounds and the second sheet the list of reactions. Each compound is identified by a local identifier consisting of "Ath_C" followed by a four-digit number, its Kegg identifier and AraCyc name. Each reaction is identified by a local identifier consisting of "Ath_R" followed by a four-digit number, its Kegg identifier and AraCyc name. The stoichiometry column describes the reaction using local compound identifier. Substrates and products are separated by the equal ("=") sign. The stoichiometry is always explicitly written even when it is one. The enzyme column lists the enzymes catalysing each reaction by their EC number.

Format: XLS Size: 404KB Download file

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Additional file 3:

Compound and reaction data of the complete (blue) metabolic network. The first sheet contains the list of compounds and the second sheet the list of reactions. Each compound is identified by a local identifier consisting of "Ath_C" followed by a four-digit number, its Kegg identifier and AraCyc name. Each reaction is identified by a local identifier consisting of "Ath_R" followed by a four-digit number, its Kegg identifier and AraCyc name. The stoichiometry column describes the reaction using local compound identifier. Substrates and products are separated by the equal ("=") sign. The stoichiometry is always explicitly written even when it is one. The enzyme column lists the enzymes catalysing each reaction by their EC number. The gene columns list genes associated to each reaction based on EC numbers.

Format: XLS Size: 737KB Download file

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Additional file 4:

Distribution of enzymes in the three metabolic networks for each Kegg pathway. The first two columns give the Kegg identifier and name of each pathway. The yellow columns give the number of enzymes from this pathway attributed to the core metabolic network and its percentage in relation to the total number of enzymes contained in the pathway. The green columns give the number of enzymes attributed to the intermediate metabolic network and its percentage in relation to the total number of enzymes. The blue column gives the number of enzymes contained in the complete network, which is equal to the total number of enzymes contained in the pathway.

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Additional file 5:

Comparison between topological properties of a classical and atomistic representation for the core (yellow) metabolic network. Red colour is used for the classical network, orange for the atomistic network. (a) Node degree distribution. (b) Average clustering coefficient distribution. (c) Betweenness centrality. (d) Closeness centrality. (e) Shared neighbours distribution. (f) Shortest path length distribution. See methods section for an explanation of network parameters.

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Additional file 6:

Annotated SBML file of the core (yellow) metabolic network.

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Additional file 7:

SBML file of the intermediate (green) metabolic network.

Format: XML Size: 716KB Download file

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Additional file 8:

SBML file of the complete (blue) metabolic network.

Format: XML Size: 1.2MB Download file

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Additional file 9:

Software and protocol for semi-automatic reconstruction (Java source code).

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