An extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks.
Cast your vote
You can rate an item by clicking the amount of stars they wish to award to this item.
When enough users have cast their vote on this item, the average rating will also be shown.
Your vote was cast
Thank you for your feedback
Thank you for your feedback
MetadataShow full item record
AbstractThe 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.
CitationAn extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks. 2011, 3 (11):1071-86 Integr Biol (Camb)
The following license files are associated with this item:
- Pathway identification by network pruning in the metabolic network of Escherichia coli.
- Authors: Gerlee P, Lizana L, Sneppen K
- Issue date: 2009 Dec 15
- METANNOGEN: compiling features of biochemical reactions needed for the reconstruction of metabolic networks.
- Authors: Gille C, Hoffmann S, Holzhütter HG
- Issue date: 2007 Jan 9
- Computing the shortest elementary flux modes in genome-scale metabolic networks.
- Authors: de Figueiredo LF, Podhorski A, Rubio A, Kaleta C, Beasley JE, Schuster S, Planes FJ
- Issue date: 2009 Dec 1
- Metabolic pathfinding using RPAIR annotation.
- Authors: Faust K, Croes D, van Helden J
- Issue date: 2009 May 1
- Reconstruction and analysis of human liver-specific metabolic network based on CNHLPP data.
- Authors: Zhao J, Geng C, Tao L, Zhang D, Jiang Y, Tang K, Zhu R, Yu H, Zhang W, He F, Li Y, Cao Z
- Issue date: 2010 Apr 5