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

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	An extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks
	Stelzer, Michael 1,2; Sun, Jibin 2,3; Kamphans, Tom 4; Fekete, Sandor P.4; Zeng, An-Ping 2,5
刊名	INTEGRATIVE BIOLOGY
	2011
卷号	3 期号:11 页码:1071-1086
关键词	DETECTING COMMUNITY STRUCTURE CONNECTIVITY STRUCTURE PATHWAYS CENTRALITY IDENTIFICATION BETWEENNESS MODULARITY ALGORITHM GRAPH WEB
英文摘要	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.
WOS标题词	Science & Technology ; Life Sciences & Biomedicine
类目[WOS]	Cell Biology
研究领域[WOS]	Cell Biology
关键词[WOS]	DETECTING COMMUNITY STRUCTURE ; CONNECTIVITY STRUCTURE ; PATHWAYS ; CENTRALITY ; IDENTIFICATION ; BETWEENNESS ; MODULARITY ; ALGORITHM ; GRAPH ; WEB
收录类别	SCI
语种	英语
WOS记录号	WOS:000296335000002
公开日期	2011-12-28
内容类型	期刊论文
源URL	[http://localhost/handle/0/198]
专题	天津工业生物技术研究所_系统与合成生物技术实验室孙际宾_期刊论文
作者单位	1.Braunschweig Univ Technol, Dept Bioinformat & Biochem, D-38106 Braunschweig, Germany 2.Helmholtz Ctr Infect Res HZI, Syst Biol Grp, D-38124 Braunschweig, Germany 3.Chinese Acad Sci, Key Lab Syst Microbial Biotechnol, Tianjin Inst Ind Biotechnol, Xiqidao Tianjin Airport Econ Area 32, Tianjin 300308, Peoples R China 4.Braunschweig Univ Technol, Dept Comp Sci, Algorithms Grp, D-38106 Braunschweig, Germany 5.Hamburg Univ Technol, Inst Bioproc & Biosyst Engn, D-21073 Hamburg, Germany
推荐引用方式 GB/T 7714	Stelzer, Michael,Sun, Jibin,Kamphans, Tom,et al. An extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks[J]. INTEGRATIVE BIOLOGY,2011,3(11):1071-1086.
APA	Stelzer, Michael,Sun, Jibin,Kamphans, Tom,Fekete, Sandor P.,&Zeng, An-Ping.(2011).An extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks.INTEGRATIVE BIOLOGY,3(11),1071-1086.
MLA	Stelzer, Michael,et al."An extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks".INTEGRATIVE BIOLOGY 3.11(2011):1071-1086.