Format

Send to

Choose Destination
Bioinformatics. 2011 May 15;27(10):1397-403. doi: 10.1093/bioinformatics/btr145. Epub 2011 Mar 23.

Mass-balanced randomization of metabolic networks.

Author information

1
University of Potsdam, Institute for Biochemistry and Biology, Potsdam, Germany. basler@mpimp-golm.mpg.de

Abstract

MOTIVATION:

Network-centered studies in systems biology attempt to integrate the topological properties of biological networks with experimental data in order to make predictions and posit hypotheses. For any topology-based prediction, it is necessary to first assess the significance of the analyzed property in a biologically meaningful context. Therefore, devising network null models, carefully tailored to the topological and biochemical constraints imposed on the network, remains an important computational problem.

RESULTS:

We first review the shortcomings of the existing generic sampling scheme-switch randomization-and explain its unsuitability for application to metabolic networks. We then devise a novel polynomial-time algorithm for randomizing metabolic networks under the (bio)chemical constraint of mass balance. The tractability of our method follows from the concept of mass equivalence classes, defined on the representation of compounds in the vector space over chemical elements. We finally demonstrate the uniformity of the proposed method on seven genome-scale metabolic networks, and empirically validate the theoretical findings. The proposed method allows a biologically meaningful estimation of significance for metabolic network properties.

PMID:
21436128
PMCID:
PMC3087954
DOI:
10.1093/bioinformatics/btr145
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center