Metabolite coupling in genome-scale metabolic networks

BMC Bioinformatics
Scott A BeckerBernhard Ø Palsson

Abstract

Biochemically detailed stoichiometric matrices have now been reconstructed for various bacteria, yeast, and for the human cardiac mitochondrion based on genomic and proteomic data. These networks have been manually curated based on legacy data and elementally and charge balanced. Comparative analysis of these well curated networks is now possible. Pairs of metabolites often appear together in several network reactions, linking them topologically. This co-occurrence of pairs of metabolites in metabolic reactions is termed herein "metabolite coupling." These metabolite pairs can be directly computed from the stoichiometric matrix, S. Metabolite coupling is derived from the matrix ŝŝT, whose off-diagonal elements indicate the number of reactions in which any two metabolites participate together, where ŝ is the binary form of S. Metabolite coupling in the studied networks was found to be dominated by a relatively small group of highly interacting pairs of metabolites. As would be expected, metabolites with high individual metabolite connectivity also tended to be those with the highest metabolite coupling, as the most connected metabolites couple more often. For metabolite pairs that are not highly coupled, we show that the number ...Continue Reading

References

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Citations

Jun 10, 2008·Nature Biotechnology·Adam M Feist, Bernhard Ø Palsson
Feb 9, 2008·Annual Review of Plant Biology·Igor G L Libourel, Yair Shachar-Hill
Feb 6, 2008·BMC Systems Biology·Scott A Becker, Bernhard O Palsson
Jul 16, 2010·BMC Systems Biology·Balaji Veeramani, Joel S Bader
Mar 1, 2007·Genome Biology·Juan Javier Díaz-MejíaLorenzo Segovia
Feb 3, 2007·Proceedings of the National Academy of Sciences of the United States of America·Natalie C DuarteBernhard Ø Palsson
Dec 11, 2008·FEMS Microbiology Reviews·Maxime DurotVincent Schachter
Nov 25, 2016·Cell Systems·Sarah W Harcum, Kelvin H Lee
Jan 9, 2014·Nature Communications·Mathias GanterJörg Stelling
Nov 6, 2009·Molecular Systems Biology·Matthew A OberhardtJason A Papin
Apr 28, 2010·FEBS Letters·Liming LiuJens Nielsen
Nov 22, 2018·BMC Systems Biology·José F HidalgoJosé M García

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