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IPM
30
YEARS OLD

“School of Biological Sciences”

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Paper   IPM / Biological Sciences / 15940
School of Biological Sciences
  Title:   CAMND: Comparative analysis of metabolic network decomposition based on previous and two new criteria, a web based application
  Author(s): 
1 . Fatemeh Yassaee Meybodi
2 . Akram Emdadi
3 . Abolfazl Rezvan
4 . Changiz Eslahchi
  Status:   Published
  Journal: Biosystems
  Vol.:  189
  Year:  2020
  Pages:   https://doi.org/10.1016/j.biosystems.2019.104081
  Supported by:  IPM
  Abstract:
Metabolic networks can model the behavior of metabolism in the cell. Since analyzing the whole metabolic networks is not easy, network modulation is an important issue to be investigated. Decomposing metabolic networks is a strategy to obtain better insight into metabolic functions. Additionally, decomposing these networks facilitates using computational methods, which are very slow when applied to the original genome-scale network. Several methods have been proposed for decomposing of the metabolic network. Therefore, it is necessary to evaluate these methods by suitable criteria. In this study, we introduce a web server package for decomposing of metabolic networks with 10 different methods, 9 datasets and the ability of computing 12 criteria, to evaluate and compare the results of different methods using ten previously defined and two new criteria which are based on Chebi ontology and Co-expression_of_Enzymes information. This package visualizes the obtained modules via “gephi” software. The ability of this package is that the user can examine whether two metabolites or reactions are in the same module or not. The functionality of the package can be easily extended to include new datasets and criteria. It also has the ability to compare the results of novel methods with the results of previously developed methods. The package is implemented in python and is available at http://eslahchilab.ir/softwares/dmn.


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