Integrative study of Arabidopsis thaliana metabolomic and transcriptomic data with the interactive MarVis-Graph software

State of the art high-throughput technologies allow comprehensive experimental studies of organism metabolism and induce the need for a convenient presentation of large heterogeneous datasets. Especially, the combined analysis and visualization of data from different high-throughput technologies rem...

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Bibliographic Details
Published in:PeerJ (San Francisco, CA) CA), 2014-03, Vol.2, p.e239-e239
Main Authors: Landesfeind, Manuel, Kaever, Alexander, Feussner, Kirstin, Thurow, Corinna, Gatz, Christiane, Feussner, Ivo, Meinicke, Peter
Format: Article
Language:English
Subjects:
Arabidopsis
Arabidopsis thaliana
Bioinformatics
Biology
Biosynthesis
Computational Biology
Computer programs
Datasets
DNA microarray
Enzymes
Experiments
Gene expression
Genomes
Metabolic network analysis
Metabolism
Metabolite fingerprinting
Metabolites
Metabolomics
Plant Science
Principal components analysis
Signal transduction
Software
Studies
Transcriptomics
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Summary:State of the art high-throughput technologies allow comprehensive experimental studies of organism metabolism and induce the need for a convenient presentation of large heterogeneous datasets. Especially, the combined analysis and visualization of data from different high-throughput technologies remains a key challenge in bioinformatics. We present here the MarVis-Graph software for integrative analysis of metabolic and transcriptomic data. All experimental data is investigated in terms of the full metabolic network obtained from a reference database. The reactions of the network are scored based on the associated data, and sub-networks, according to connected high-scoring reactions, are identified. Finally, MarVis-Graph scores the detected sub-networks, evaluates them by means of a random permutation test and presents them as a ranked list. Furthermore, MarVis-Graph features an interactive network visualization that provides researchers with a convenient view on the results. The key advantage of MarVis-Graph is the analysis of reactions detached from their pathways so that it is possible to identify new pathways or to connect known pathways by previously unrelated reactions. The MarVis-Graph software is freely available for academic use and can be downloaded at: http://marvis.gobics.de/marvis-graph.
ISSN:2167-8359
2167-8359
DOI:10.7717/peerj.239