Hierarchical Organization of Modularity in Metabolic Networks
TLDR
It is shown that the metabolic networks of 43 distinct organisms are organized into many small, highly connected topologic modules that combine in a hierarchical manner into larger, less cohesive units, with their number and degree of clustering following a power law.Abstract:
Spatially or chemically isolated functional modules composed of several cellular components and carrying discrete functions are considered fundamental building blocks of cellular organization, but their presence in highly integrated biochemical networks lacks quantitative support Here, we show that the metabolic networks of 43 distinct organisms are organized into many small, highly connected topologic modules that combine in a hierarchical manner into larger, less cohesive units, with their number and degree of clustering following a power law Within Escherichia coli, the uncovered hierarchical modularity closely overlaps with known metabolic functions The identified network architecture may be generic to system-level cellular organizationread more
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References
More filters
Journal ArticleDOI
Robustness in bacterial chemotaxis
TL;DR: This work focuses on how response and adaptation to attractant signals vary with systematic changes in the intracellular concentration of the components of the chemotaxis network, and finds that some properties show strong variations in response to varying protein concentrations.
Journal ArticleDOI
Self-organization and identification of Web communities
TL;DR: This work shows that the Web self-organizes and its link structure allows efficient identification of communities and is significant because no central authority or process governs the formation and structure of hyperlinks.
Journal ArticleDOI
The small world inside large metabolic networks
Andreas Wagner,David A. Fell +1 more
TL;DR: In this article, a graph theoretical analysis of the E. coli metabolic network was performed and it was shown that the connectivity of the metabolites follows a power law, another unusual but by no means rare statistical distribution, which provides an objective criterion for the centrality of the tricarboxylic acid cycle to metabolism.
Journal ArticleDOI
A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks.
TL;DR: This work analyzes the interplay between the pentose phosphate pathway (PPP) and glycolysis to define and comprehensively describe all metabolic routes that are both stoichiometrically and thermodynamically feasible for a group of enzymes.
Journal ArticleDOI
Theory for the Systemic Definition of Metabolic Pathways and their use in Interpreting Metabolic Function from a Pathway-Oriented Perspective
TL;DR: This study presents the theoretical foundations for the identification of the unique set of systemically independent biochemical pathways, termed extreme pathways, based on system stochiometry and limited thermodynamics, and can be used to represent any flux distribution achievable by the metabolic network.