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

2.50
Hdl Handle:
http://hdl.handle.net/10033/324802
Title:
An extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks.
Authors:
Stelzer, Michael; Sun, Jibin; Kamphans, Tom; Fekete, Sándor P; Zeng, An-Ping ( 0000-0001-9768-7096 )
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.
Citation:
An extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks. 2011, 3 (11):1071-86 Integr Biol (Camb)
Journal:
Integrative biology : quantitative biosciences from nano to macro
Issue Date:
Nov-2011
URI:
http://hdl.handle.net/10033/324802
DOI:
10.1039/c1ib00008j
PubMed ID:
21952610
Type:
Article
Language:
en
ISSN:
1757-9708
Appears in Collections:
Publications of RG Systems Biology (SBIO)

Full metadata record

DC FieldValue Language
dc.contributor.authorStelzer, Michaelen
dc.contributor.authorSun, Jibinen
dc.contributor.authorKamphans, Tomen
dc.contributor.authorFekete, Sándor Pen
dc.contributor.authorZeng, An-Pingen
dc.date.accessioned2014-08-14T12:52:18Z-
dc.date.available2014-08-14T12:52:18Z-
dc.date.issued2011-11-
dc.identifier.citationAn extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks. 2011, 3 (11):1071-86 Integr Biol (Camb)en
dc.identifier.issn1757-9708-
dc.identifier.pmid21952610-
dc.identifier.doi10.1039/c1ib00008j-
dc.identifier.urihttp://hdl.handle.net/10033/324802-
dc.description.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.en
dc.language.isoenen
dc.rightsArchived with thanks to Integrative biology : quantitative biosciences from nano to macroen
dc.subject.meshAlgorithmsen
dc.subject.meshAspergillus nigeren
dc.subject.meshComputational Biologyen
dc.subject.meshDatabases, Factualen
dc.subject.meshDatabases, Geneticen
dc.subject.meshEscherichia colien
dc.subject.meshGenomeen
dc.subject.meshGlucoseen
dc.subject.meshHumansen
dc.subject.meshMetabolic Networks and Pathwaysen
dc.subject.meshModels, Biologicalen
dc.subject.meshSoftwareen
dc.titleAn extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks.en
dc.typeArticleen
dc.identifier.journalIntegrative biology : quantitative biosciences from nano to macroen

Related articles on PubMed

This item is licensed under a Creative Commons License
Creative Commons
All Items in HZI are protected by copyright, with all rights reserved, unless otherwise indicated.