Chapter title |
Exploring Plant Co-Expression and Gene-Gene Interactions with CORNET 3.0.
|
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Chapter number | 11 |
Book title |
Plant Genomics Databases
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Published in |
Methods in molecular biology, January 2017
|
DOI | 10.1007/978-1-4939-6658-5_11 |
Pubmed ID | |
Book ISBNs |
978-1-4939-6656-1, 978-1-4939-6658-5
|
Authors |
Michiel Van Bel, Frederik Coppens |
Editors |
Aalt D.J van Dijk |
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/ . |
Mendeley readers
Geographical breakdown
Country | Count | As % |
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Unknown | 14 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
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Researcher | 4 | 29% |
Student > Master | 4 | 29% |
Unspecified | 1 | 7% |
Student > Bachelor | 1 | 7% |
Other | 1 | 7% |
Other | 2 | 14% |
Unknown | 1 | 7% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 7 | 50% |
Biochemistry, Genetics and Molecular Biology | 4 | 29% |
Computer Science | 1 | 7% |
Unspecified | 1 | 7% |
Unknown | 1 | 7% |