The strength of chemical linkage as a criterion for pruning metabolic graphs.

Bioinformatics
Wanding Zhou, Luay Nakhleh

Abstract

A metabolic graph represents the connectivity patterns of a metabolic system, and provides a powerful framework within which the organization of metabolic reactions can be analyzed and elucidated. A common practice is to prune (i.e. remove nodes and edges) the metabolic graph prior to any analysis in order to eliminate confounding signals from the representation. Currently, this pruning process is carried out in an ad hoc fashion, resulting in discrepancies and ambiguities across studies. We propose a biochemically informative criterion, the strength of chemical linkage (SCL), for a systematic pruning of metabolic graphs. By analyzing the metabolic graph of Escherichia coli, we show that thresholding SCL is powerful in selecting the conventional pathways' connectivity out of the raw network connectivity when the network is restricted to the reactions collected from these pathways. Further, we argue that the root of ambiguity in pruning metabolic graphs is in the continuity of the amount of chemical content that can be conserved in reaction transformation patterns. Finally, we demonstrate how biochemical pathways can be inferred efficiently if the search procedure is guided by SCL.

References

Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Oct 18, 2000·Nature·H JeongA L Barabási
Aug 28, 2001·Proceedings. Biological Sciences·A Wagner, D A Fell
Aug 31, 2002·Science·E RavaszA L Barabási
Oct 30, 2003·Briefings in Bioinformatics·Yves DevilleShoshana J Wodak
Dec 19, 2003·Nucleic Acids Research·Christian LemerShoshana J Wodak
Dec 2, 2004·Bioinformatics·S A RahmanDietmar Schomburg
Jan 15, 2005·BMC Bioinformatics·Dongxiao Zhu, Zhaohui S Qin
May 21, 2005·Physical Review Letters·Reiko Tanaka
Jul 28, 2005·Journal of Biochemistry·Masanori Arita
Dec 13, 2005·Journal of Molecular Biology·Didier CroesJacques van Helden
Mar 25, 2006·BMC Bioinformatics·Thomas J LeePeter D Karp
Aug 19, 2006·BMC Bioinformatics·Jing ZhaoYi-Xue Li
Mar 1, 2007·Genome Biology·Juan Javier Díaz-MejíaLorenzo Segovia
Aug 29, 2007·BMC Bioinformatics·Jing ZhaoYi-Xue Li
Jul 18, 2008·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Torsten Blum, Oliver Kohlbacher
Jan 23, 2009·Journal of the Royal Society, Interface·Petter Holme
Mar 14, 2009·Journal of Molecular Biology·Karoline FaustJacques van Helden
Aug 19, 2010·Journal of Chemical Information and Modeling·John D CrabtreeTina M Kouri

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Citations

Jan 10, 2017·PloS One·Yiran HuangJianyi Wang
Feb 3, 2021·PLoS Computational Biology·Yiran HuangFengfeng Zhou

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