- Abstract:
- Structural and functional analysis of genomebased large-scale metabolic networks is important for understanding the design principles and regulation of the metabolism at a system level. The metabolic network is conventionally considered to be highly integrated and very complex. A rational reduction of the metabolic network to its core structure and a deeper understanding of its functional modules are important. Results: In this work, we show that the metabolites in a metabolic network are far from fully connected. A connectivity structure consisting of four major subsets of metabolites and reactions, i.e. a fully connected sub-network, a substrate subset, a product subset and an isolated subset is found to exist in metabolic networks of 65 fully sequenced organisms. The largest fully connected part of a metabolic network, called the giant strong component (GSC) , represents the most complicated part and the core of the network and has the feature of scale-free networks. The average path length of the whole network is primarily determined by that of the GSC. For most of the organisms, GSC normally contains less than one-third of the nodes of the network. This connectivity structure is very similar to the bow-tie structure of World Wide Web. Our results indicate that the bow-tie structure may be common for largescale directed networks. More importantly, the uncovered structure feature makes a structural and functional analysis of large-scale metabolic network more amenable. As shown in this work, comparing the closeness centrality of the nodes in the GSC can identify the most central metabolites of a metabolic network. To quantitatively characterize the overall connection structure of the GSC we introduced the term overall closeness centralization index (OCCI) . OCCI correlates well with the average path length of the GSC and is a useful parameter for a system-level comparison of metabolic networks of different organisms.
- Links To Paper
- 1st Link
- Bibtex format
- @Article{EDI-INF-RR-0986,
- author = {
Hongwu Ma
and An-Ping Zeng
},
- title = {The connectivity structure, giant strong component and centrality of metabolic networks},
- journal = {Bioinformatics},
- publisher = {Oxford University Press},
- year = 2003,
- volume = {19(11)},
- pages = {1423-1430},
- doi = {10.1093/bioinformatics/btg177},
- url = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/11/1423},
- }
|
