A network perspective on metabolic inconsistency.

BMC Systems Biology
Nikolaus SonnenscheinMarc-Thorsten Hütt

Abstract

Integrating gene expression profiles and metabolic pathways under different experimental conditions is essential for understanding the coherence of these two layers of cellular organization. The network character of metabolic systems can be instrumental in developing concepts of agreement between expression data and pathways. A network-driven interpretation of gene expression data has the potential of suggesting novel classifiers for pathological cellular states and of contributing to a general theoretical understanding of gene regulation. Here, we analyze the coherence of gene expression patterns and a reconstruction of human metabolism, using consistency scores obtained from network and constraint-based analysis methods. We find a surprisingly strong correlation between the two measures, demonstrating that a substantial part of inconsistencies between metabolic processes and gene expression can be understood from a network perspective alone. Prompted by this finding, we investigate the topological context of the individual biochemical reactions responsible for the observed inconsistencies. On this basis, we are able to separate the differential contributions that bear physiological information about the system, from the unspe...Continue Reading

References

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Oct 20, 2004·Metabolic Engineering·Mats AkessonJens Nielsen
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Oct 13, 2010·Hypertension·Sheerazed BoulkrounMaria-Christina Zennaro
Mar 17, 2011·BMC Systems Biology·Nikolaus SonnenscheinMarc-Thorsten Hütt

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Citations

Apr 15, 2014·British Journal of Clinical Pharmacology·Marc-Thorsten Hütt
Jan 1, 2012·Metabolites·Nikolaus SonnenscheinMarc-Thorsten Hütt
Jun 4, 2013·Nature Reviews. Microbiology·G Lynn LawMichael G Katze
May 6, 2019·PLoS Computational Biology·Anne GrimbsMarc-Thorsten Hütt
Aug 8, 2015·Briefings in Bioinformatics·Mufassra NazMartin Hofmann-Apitius
Jan 29, 2021·PLoS Computational Biology·Zachary B HaimanBernhard O Palsson

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Software Mentioned

Human Recon 1
GIMME
COMETE
GIMME ( Gene Inactivity Moderated by Metabolism and Expression

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