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Plant Genomics Databases pp 201–212Cite as

Exploring Plant Co-Expression and Gene-Gene Interactions with CORNET 3.0

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1533))

Abstract

Selecting and filtering a reference expression and interaction dataset when studying specific pathways and regulatory interactions can be a very time-consuming and error-prone task. In order to reduce the duplicated efforts required to amass such datasets, we have created the CORNET (CORrelation NETworks) platform which allows for easy access to a wide variety of data types: coexpression data, protein-protein interactions, regulatory interactions, and functional annotations. The CORNET platform outputs its results in either text format or through the Cytoscape framework, which is automatically launched by the CORNET website.

CORNET 3.0 is the third iteration of the web platform designed for the user exploration of the coexpression space of plant genomes, with a focus on the model species Arabidopsis thaliana. Here we describe the platform: the tools, data, and best practices when using the platform. We indicate how the platform can be used to infer networks from a set of input genes, such as upregulated genes from an expression experiment. By exploring the network, new target and regulator genes can be discovered, allowing for follow-up experiments and more in-depth study. We also indicate how to avoid common pitfalls when evaluating the networks and how to avoid over interpretation of the results.

All CORNET versions are available at http://bioinformatics.psb.ugent.be/cornet/.

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Acknowledgments

We would like to thank Stefanie De Bodt and Klaas Vandepoele for their helpful suggestions.

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Authors and Affiliations

  1. Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium

    Michiel Van Bel & Frederik Coppens

  2. Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium

    Michiel Van Bel & Frederik Coppens

Authors
  1. Michiel Van Bel
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  2. Frederik Coppens
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Corresponding author

Correspondence to Michiel Van Bel .

Editor information

Editors and Affiliations

  1. PRI Bioscience, Biometris and Bioinformatics, Wageningen University & Research Wageningen, Wageningen, The Netherlands

    Aalt D.J van Dijk

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Van Bel, M., Coppens, F. (2017). Exploring Plant Co-Expression and Gene-Gene Interactions with CORNET 3.0. In: van Dijk, A. (eds) Plant Genomics Databases. Methods in Molecular Biology, vol 1533. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6658-5_11

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  • DOI: https://doi.org/10.1007/978-1-4939-6658-5_11

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6656-1

  • Online ISBN: 978-1-4939-6658-5

  • eBook Packages: Springer Protocols

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