A Data Integration and Visualization Resource for the Metabolic Network of Synechocystis sp. PCC 6803

Data integration is a central activity in systems biology. The integration of genomic, transcript, protein, metabolite, flux, and computational data yields unprecedented information about the system level functioning of organisms. Often, data integration is done purely computationally, leaving the u...

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Bibliographic Details
Published in:Plant physiology (Bethesda) 2014-03, Vol.164 (3), p.1111-1121
Main Authors: Maarleveld, Timo R., Boele, Joost, Bruggeman, Frank J., Teusink, Bas
Format: Article
Language:English
Subjects:
Adaptation, Physiological
Biofuels
Breakthrough Technologies
Cellular metabolism
Darkness
Data visualization
Databases as Topic
Datasets
Genes, Bacterial
Glycogen
Identifiers
Metabolic Flux Analysis
Metabolic Networks and Pathways - genetics
Metabolism
Metabolites
Modeling
Models, Biological
Oligonucleotide Array Sequence Analysis
Photosynthesis
Synechocystis - genetics
Synechocystis - metabolism
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Summary:Data integration is a central activity in systems biology. The integration of genomic, transcript, protein, metabolite, flux, and computational data yields unprecedented information about the system level functioning of organisms. Often, data integration is done purely computationally, leaving the user with little insight in addition to statistical information. In this article, we present a visualization tool for the metabolic network of Synechocystis sp. PCC 6803, an important model cyanobacterium for sustainable biofuel production. We illustrate how this metabolic map can be used to integrate experimental and computational data for Synechocystis sp. PCC 6803 systems biology and metabolic engineering studies. Additionally, we discuss how this map, and the software infrastructure that we supply with it, can be used in the development of other organism-specific metabolic network visualizations. In addition to the Python console package VoNDA (http://vonda.sf.net), we provide a working demonstration of the interactive metabolic map and the associated Synechocystis sp. PCC 6803 genome-scale stoichiometric model, as well as various ready-to-visualize microarray data sets, at http://f-a-m-e.org/synechocytis.
ISSN:0032-0889
1532-2548
1532-2548
DOI:10.1104/pp.113.224394