A modular approach to reconstructing genome-scale metabolic networks

A genome-scale and metabolic network technology, which is applied in the field of module division for reconstructing genome-scale metabolic networks, can solve problems such as the inability to reveal the hierarchical structure

Active Publication Date: 2017-11-28
TIANJIN NORMAL UNIVERSITY
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  • Abstract
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  • Application Information

AI Technical Summary

Problems solved by technology

Methods based on modularity indicators can produce results close to the optimal solution but fail to reveal its hierarchical structure at different levels

Method used

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  • A modular approach to reconstructing genome-scale metabolic networks
  • A modular approach to reconstructing genome-scale metabolic networks
  • A modular approach to reconstructing genome-scale metabolic networks

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Embodiment 1

[0079] A method for modularizing the reconstruction of genome-scale metabolic networks, comprising:

[0080] (1) Create a reaction graph:

[0081](a) Remove circulating metabolites and isolated reactions in the metabolic network, where circulating metabolites mainly refer to metabolites that can circulate globally in the cell, such as ATP, ADP, phosphate, diphosphate, NADP, NADPH, CO 2 , NAD, NADH, O 2 etc.; an isolated reaction is one that is not linked to any other reaction.

[0082] (b) Converting the network into a reaction graph based on the metabolite connections for each reaction. Specific method: If the product of reaction A is the same as the reactant of reaction B, a one-way connection from reaction A to reaction B can be established, which can be expressed as A->B; when there are both A->B and B->A When there are two connections, the two connections can be merged into a bidirectional connection AB.

[0083] (2) Initially decouple the network according to the cla...

Embodiment 2

[0103] Practical application of the method for module division of the reconstructed genome-scale metabolic network disclosed in the present invention

[0104] This method was used in the module division of the genome-scale metabolic network reconstruction of Eriocheir sinensis-eyestalk. The model adopted is that the genome-scale metabolic network of Eriocheir sinensis-eyestalk reconstructed contains 1304 reactions, and the number of related reactions after removing circulating metabolites is 1053. First, the metabolic network is divided into several weak linkers with pajek software ( WCCs), the network is decoupled into 66 weak linkers through the calculation of weak linkers, of which there are only 6 larger weak linkers containing more than 10 reactions, and the largest weak linker contains 774 reactions (such as figure 2 shown), accounting for about 74% of the total number of reactions in the metabolic network. On the basis of the calculation of the weak link, apply the me...

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Abstract

The invention discloses a method for dividing modules of a reconstructed genome-scale metabolic network. The method mainly comprises the steps of establishing a response diagram, primarily decoupling the network according to a classification tree and optimizing network decoupling. The method integrates the advantages of a hierarchical clustering method and a nonhierarchical clustering method, a hierarchical structure of the metabolic network is obtained by generating a clustering tree, hierarchy of the biological metabolic network is met, and through optimization of modularization indexes, the best decoupling result is obtained. Accordingly, hierarchy and modularity of the network are both achieved, the characteristics of a biological network are met, and the best decoupling result is obtained structurally.

Description

[0001] This invention is funded by the National Natural Science Foundation of China (NO.21106095), the talent introduction fund of Tianjin Normal University, and the project of "introducing more than 1,000 high-level talents in three years" in Tianjin. technical field [0002] The invention belongs to the technical field of bioinformatics of network module division, and relates to a method for module division of a reconstructed genome-scale metabolic network. Background technique [0003] Network modularization, or network decoupling, refers to the process of decomposing a complex network into structurally and functionally independent subsets (called modules). With the rapid development of high-throughput technologies such as genome sequencing, massive biological data are generated and accumulated, which makes it possible to construct large-scale biological networks and express them as biological systems with complex structures. These biological networks usually have a large...

Claims

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Application Information

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Patent Type & AuthorityPatents(China)
IPC IPC(8): G06F19/18
Inventor郝彤于爱玲孙金生
OwnerTIANJIN NORMAL UNIVERSITY