dorsal/arxiv
View SchemaHierarchical modularity of nested bow-ties in metabolic networks
| Authors | Jing Zhao, Hong Yu, Jian-Hua Luo, Zhi-Wei Cao, Yi-Xue Li |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0605003 |
| URL | https://arxiv.org/abs/q-bio/0605003 |
| Journal | BMC Bioinformatics 2006, 7:386 |
Abstract
The exploration of the structural topology and the organizing principles of genome-based large-scale metabolic networks is essential for studying possible relations between structure and functionality of metabolic networks. Topological analysis of graph models has often been applied to study the structural characteristics of complex metabolic networks.In this work, metabolic networks of 75 organisms were investigated from a topological point of view. Network decomposition of three microbes (Escherichia coli, Aeropyrum pernix and Saccharomyces cerevisiae) shows that almost all of the sub-networks exhibit a highly modularized bow-tie topological pattern similar to that of the global metabolic networks. Moreover, these small bow-ties are hierarchically nested into larger ones and collectively integrated into a large metabolic network, and important features of this modularity are not observed in the random shuffled network. In addition, such a bow-tie pattern appears to be present in certain chemically isolated functional modules and spatially separated modules including carbohydrate metabolism, cytosol and mitochondrion respectively. The highly modularized bow-tie pattern is present at different levels and scales, and in different chemical and spatial modules of metabolic networks, which is likely the result of the evolutionary process rather than a random accident. Identification and analysis of such a pattern is helpful for understanding the design principles and facilitate the modelling of metabolic networks.
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"abstract": "The exploration of the structural topology and the organizing principles of\ngenome-based large-scale metabolic networks is essential for studying possible\nrelations between structure and functionality of metabolic networks.\nTopological analysis of graph models has often been applied to study the\nstructural characteristics of complex metabolic networks.In this work,\nmetabolic networks of 75 organisms were investigated from a topological point\nof view. Network decomposition of three microbes (Escherichia coli, Aeropyrum\npernix and Saccharomyces cerevisiae) shows that almost all of the sub-networks\nexhibit a highly modularized bow-tie topological pattern similar to that of the\nglobal metabolic networks. Moreover, these small bow-ties are hierarchically\nnested into larger ones and collectively integrated into a large metabolic\nnetwork, and important features of this modularity are not observed in the\nrandom shuffled network. In addition, such a bow-tie pattern appears to be\npresent in certain chemically isolated functional modules and spatially\nseparated modules including carbohydrate metabolism, cytosol and mitochondrion\nrespectively. The highly modularized bow-tie pattern is present at different\nlevels and scales, and in different chemical and spatial modules of metabolic\nnetworks, which is likely the result of the evolutionary process rather than a\nrandom accident. Identification and analysis of such a pattern is helpful for\nunderstanding the design principles and facilitate the modelling of metabolic\nnetworks.",
"arxiv_id": "q-bio/0605003",
"authors": [
"Jing Zhao",
"Hong Yu",
"Jian-Hua Luo",
"Zhi-Wei Cao",
"Yi-Xue Li"
],
"categories": [
"q-bio.MN"
],
"journal_ref": "BMC Bioinformatics 2006, 7:386",
"title": "Hierarchical modularity of nested bow-ties in metabolic networks",
"url": "https://arxiv.org/abs/q-bio/0605003"
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