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Bioinformatics Advance Access published online on March 6, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm074
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Metabolic Network Properties Help Assign Weights to Elementary Modes to Understand Physiological Flux Distributions

Qingzhao Wang {dagger}, Yudi Yang {dagger}, Hongwu Ma and Xueming Zhao *

Metabolic Engineering Laboratory, Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People’s Republic of China.

*To whom correspondence should be addressed. Xueming Zhao, E-mail: xmzhao{at}tju.edu.cn


  Abstract

Motivation: Elementary modes (EMs) analysis has been well established. The existing methodologies for assigning weights to EMs can not be directly applied for large-scale metabolic networks, since the tremendous number of modes would make the computation a time-consuming or even an impossible mission. Therefore, developing more efficient methods to deal with large set of EMs is urgent.

Results: We develop a method to evaluate the performance of employing a subset of the elementary modes to reconstruct a real flux distribution by using the relative error between the real flux vector and the reconstructed one as an indicator. We have found a power function relationship between the decrease of relative error and the increase of the number of the selecting EMs, and a logarithmic relationship between the increases of the number of non-zero weighted EMs and that of the number of the selecting EMs. Our discoveries show that it is possible to reconstruct a given flux distribution by a selected subset of EMs from a large metabolic network and furthermore, they help us identify the "governing modes" to represent the cellular metabolism for such a condition.

Associate Editor: Prof. Alfonso Valencia

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

Received on October 31, 2006; revised on February 21, 2007; accepted on February 24, 2007

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