Analysis on relationship between extreme pathways and correlated reaction sets

Xi, Yanping, Chen, Yi-Ping Phoebe, Cao, Ming, Wang, Weirong and Wang, Fei 2009, Analysis on relationship between extreme pathways and correlated reaction sets, BMC bioinformatics, vol. 10, no. Supplement 1, pp. S58-S71.

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Title Analysis on relationship between extreme pathways and correlated reaction sets
Author(s) Xi, Yanping
Chen, Yi-Ping Phoebe
Cao, Ming
Wang, Weirong
Wang, Fei
Journal name BMC bioinformatics
Volume number 10
Issue number Supplement 1
Start page S58
End page S71
Publisher BioMed Central Ltd
Place of publication London, England
Publication date 2009-01-30
ISSN 1471-2105
Keyword(s) Metabolic networks
Constraint-based modelling
Extreme pathways
Correlated reaction sets
Summary Background: Constraint-based modeling of reconstructed genome-scale metabolic networks has been successfully applied on several microorganisms. In constraint-based modeling, in order to characterize all allowable phenotypes, network-based pathways, such as extreme pathways and elementary flux modes, are defined. However, as the scale of metabolic network rises, the number of extreme pathways and elementary flux modes increases exponentially. Uniform random sampling solves this problem to some extent to study the contents of the available phenotypes. After uniform random sampling, correlated reaction sets can be identified by the dependencies between reactions derived from sample phenotypes. In this paper, we study the relationship between extreme pathways and correlated reaction sets.

Results: Correlated reaction sets are identified for E. coli core, red blood cell and Saccharomyces cerevisiae metabolic networks respectively. All extreme pathways are enumerated for the former two metabolic networks. As for Saccharomyces cerevisiae metabolic network, because of the large scale, we get a set of extreme pathways by sampling the whole extreme pathway space. In most cases, an extreme pathway covers a correlated reaction set in an 'all or none' manner, which means either all reactions in a correlated reaction set or none is used by some extreme pathway. In rare cases, besides the 'all or none' manner, a correlated reaction set may be fully covered by combination of a few extreme pathways with related function, which may bring redundancy and flexibility to improve the survivability of a cell. In a word, extreme pathways show strong complementary relationship on usage of reactions in the same correlated reaction set.

Conclusion: Both extreme pathways and correlated reaction sets are derived from the topology information of metabolic networks. The strong relationship between correlated reaction sets and extreme pathways suggests a possible mechanism: as a controllable unit, an extreme pathway is regulated by its corresponding correlated reaction sets, and a correlated reaction set is further regulated by the organism's regulatory network.
Notes Paper presented at The Seventh Asia Pacific Bioinformatics Conference (APBC 2009)
Language eng
Field of Research 080301 Bioinformatics Software
Socio Economic Objective 860903 Veterinary Pharmaceutical Treatments (e.g. Antibiotics)
HERDC Research category C1 Refereed article in a scholarly journal
ERA Research output type C Journal article
HERDC collection year 2009
Copyright notice ©2009, Xi et al
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Document type: Journal Article
Collection: School of Information Technology
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