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
Citations
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Computational Strategies for a System-Level Understanding of Metabolism
Paolo Cazzaniga,Chiara Damiani,Daniela Besozzi,Riccardo Colombo,Marco S. Nobile,Daniela Gaglio,Dario Pescini,Sara Molinari,Giancarlo Mauri,Lilia Alberghina,Marco Vanoni +10 more
TL;DR: This review provides an up-to-date description of the computational methods available for the analysis of metabolic pathways, discussing their main advantages and drawbacks and describing some computational approaches to gain new biological knowledge or to formulate hypotheses.
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Phylogenetic distances are encoded in networks of interacting pathways
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Introduction to Philosophy of Complex Systems
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Protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster: Large‐scale organization and robustness
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TL;DR: A systematic analysis of topological structure and robustness was performed on theprotein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster, showing that the three protein interaction networks have a scale‐free and high‐degree clustering nature as the consequence of their hierarchical organization.
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