Exploring plant co-expression and gene-gene Interactions with CORNET 3.0
(2017)
Plant genomics databases : methods and protocols.
In Methods in Molecular Biology
1533.
p.201-212
- Author
- Michiel Van Bel (UGent) and Frederik Coppens (UGent)
- Organization
- 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/ .
- Keywords
- Coexpression, Data integration, Networks, Plants, Protein-protein interactions
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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-8500212
- MLA
- Van Bel, Michiel, and Frederik Coppens. “Exploring Plant Co-Expression and Gene-Gene Interactions with CORNET 3.0.” Plant Genomics Databases : Methods and Protocols, edited by Aalt DJ van Dijk, vol. 1533, Springer, 2017, pp. 201–12, doi:10.1007/978-1-4939-6658-5_11.
- APA
- Van Bel, M., & Coppens, F. (2017). Exploring plant co-expression and gene-gene Interactions with CORNET 3.0. In A. D. van Dijk (Ed.), Plant genomics databases : methods and protocols (Vol. 1533, pp. 201–212). https://doi.org/10.1007/978-1-4939-6658-5_11
- Chicago author-date
- Van Bel, Michiel, and Frederik Coppens. 2017. “Exploring Plant Co-Expression and Gene-Gene Interactions with CORNET 3.0.” In Plant Genomics Databases : Methods and Protocols, edited by Aalt DJ van Dijk, 1533:201–12. New York, NY, USA: Springer. https://doi.org/10.1007/978-1-4939-6658-5_11.
- Chicago author-date (all authors)
- Van Bel, Michiel, and Frederik Coppens. 2017. “Exploring Plant Co-Expression and Gene-Gene Interactions with CORNET 3.0.” In Plant Genomics Databases : Methods and Protocols, ed by. Aalt DJ van Dijk, 1533:201–212. New York, NY, USA: Springer. doi:10.1007/978-1-4939-6658-5_11.
- Vancouver
- 1.Van Bel M, Coppens F. Exploring plant co-expression and gene-gene Interactions with CORNET 3.0. In: van Dijk AD, editor. Plant genomics databases : methods and protocols. New York, NY, USA: Springer; 2017. p. 201–12.
- IEEE
- [1]M. Van Bel and F. Coppens, “Exploring plant co-expression and gene-gene Interactions with CORNET 3.0,” in Plant genomics databases : methods and protocols, vol. 1533, A. D. van Dijk, Ed. New York, NY, USA: Springer, 2017, pp. 201–212.
@incollection{8500212, 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/ .}}, author = {{Van Bel, Michiel and Coppens, Frederik}}, booktitle = {{Plant genomics databases : methods and protocols}}, editor = {{van Dijk, Aalt DJ}}, isbn = {{9781493966561}}, issn = {{1064-3745}}, keywords = {{Coexpression,Data integration,Networks,Plants,Protein-protein interactions}}, language = {{und}}, pages = {{201--212}}, publisher = {{Springer}}, series = {{Methods in Molecular Biology}}, title = {{Exploring plant co-expression and gene-gene Interactions with CORNET 3.0}}, url = {{http://doi.org/10.1007/978-1-4939-6658-5_11}}, volume = {{1533}}, year = {{2017}}, }
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