Research article
Accelerating the reconstruction of genome-scale metabolic networks
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* Corresponding author: Bas Teusink Bas.Teusink@nizo.nl
1 Center for Molecular and Biomolecular Informatics, Radboud University Nijmegen, P.O.Box 9010, 6500GL Nijmegen, The Netherlands
2 NIZO food research BV, P.O.Box 20, 6710BA, Ede, The Netherlands
3 Wageningen Center for Food Sciences, P.O.Box 557, 6700AN Wageningen, The Netherlands
4 Present address: Friesland Foods Corporate Research, Deventer, The Netherlands
BMC Bioinformatics 2006, 7:296 doi:10.1186/1471-2105-7-296
Published: 13 June 2006Additional files
Additional File 1:
1 has been uploaded as a Microsoft Excel file containing eight worksheets: 1. Orthology prediction: List of orthologous gene pairs between L. lactis, E. coli, B. subtilis and L. plantarum. Orthologs were predicted by applying the Inparanoid algorithm, using default settings. 2. Overlap AUTOGRAPH and Oliveira: Orthologous groups of genes from the Oliveira network and their orthologs with associated reactions. The reactions associated to the L. lactis genes in the Oliveira network are indicated under "Oliveira". 3. Unique genes for AUTOGRAPH: Orthologous groups of genes containing the L. lactis query genes (from Genbank) which are not incorporated into the Oliveira network, and their orthologs with associated reactions. L. lactis genes were classified into three different groups: (i) transport: all genes associated to transport reactions (ii) specific: incorporation of these genes and their associated reactions would potentially lead to additional biochemistry and hence possibly different model predictions and (iii) choice: these genes and associated reactions would lead to a higher resolution of the network, i.e. would specify reactions that are lumped into an overall reaction in the Oliveira network. 4. Unique specific reactions: List of unique specific reactions that are associated to L. lactis genes which are not incorporated into the Oliveira network. 5. Examples and literature support: Examples of predicted orthologs with literature support for L. lactis genes which are not incorporated into the Oliveira network. 6. Abbreviations E. coli: Compound information (including compound abbreviations) of reactions which are associated to E. coli genes. 7. Abbreviations B. subtilis: Compound information (including compound abbreviations) of reactions which are associated to B. subtilis genes. 8. Abbreviations L. plantarum: Compound information (including compound abbreviations) of reactions which are associated to L. plantarum genes.
Format: XLS Size: 1.4MB Download file
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