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A guide to CORNET for the construction of coexpression and protein-protein interaction networks

Stefanie De Bodt (UGent) and Dirk Inzé (UGent)
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Biotechnology for a sustainable economy (Bio-Economy)
Abstract
To enable easy access and interpretation of heterogenous and scattered data, we have developed a user-friendly tool for data mining and integration in Arabidopsis thaliana, designated CORrelation NETworks (acronym CORNET), allowing browsing of microarray data, construction of coexpression and protein–protein interactions (PPIs), analysis of gene association and transcription factor (TF) regulatory networks, and exploration of diverse functional annotations. CORNET consists of three tools that can be used individually or in combination, namely, the coexpression tool, the PPI tool, and the TF tool. Different search options are implemented to enable the creation of networks centered around multiple input genes or proteins. Functional annotation resources are included to retrieve relevant literature, phenotypes, localization, gene ontology, plant ontology, and biological pathways. Networks and associated evidence of the majority of the currently available data types are visualized in Cytoscape. CORNET is available at https://bioinformatics.psb.ugent.be/cornet.
Keywords
Coexpression, Plants, Networks, Protein–protein interactions

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Chicago
De Bodt, Stefanie, and Dirk Inzé. 2013. “A Guide to CORNET for the Construction of Coexpression and Protein-protein Interaction Networks.” In Jasmonate Signaling : Methods and Protocols, ed. Alain Goossens and Laurens Pauwels, 1011:327–343. New York, NY, USA: Humana Press.
APA
De Bodt, Stefanie, & Inzé, D. (2013). A guide to CORNET for the construction of coexpression and protein-protein interaction networks. In Alain Goossens & L. Pauwels (Eds.), Jasmonate signaling : methods and protocols (Vol. 1011, pp. 327–343). New York, NY, USA: Humana Press.
Vancouver
1.
De Bodt S, Inzé D. A guide to CORNET for the construction of coexpression and protein-protein interaction networks. In: Goossens A, Pauwels L, editors. Jasmonate signaling : methods and protocols. New York, NY, USA: Humana Press; 2013. p. 327–43.
MLA
De Bodt, Stefanie, and Dirk Inzé. “A Guide to CORNET for the Construction of Coexpression and Protein-protein Interaction Networks.” Jasmonate Signaling : Methods and Protocols. Ed. Alain Goossens & Laurens Pauwels. Vol. 1011. New York, NY, USA: Humana Press, 2013. 327–343. Print.
@incollection{3215099,
  abstract     = {To enable easy access and interpretation of heterogenous and scattered data, we have developed a user-friendly tool for data mining and integration in Arabidopsis thaliana, designated CORrelation NETworks (acronym CORNET), allowing browsing of microarray data, construction of coexpression and protein--protein interactions (PPIs), analysis of gene association and transcription factor (TF) regulatory networks, and exploration of diverse functional annotations. CORNET consists of three tools that can be used individually or in combination, namely, the coexpression tool, the PPI tool, and the TF tool. Different search options are implemented to enable the creation of networks centered around multiple input genes or proteins. Functional annotation resources are included to retrieve relevant literature, phenotypes, localization, gene ontology, plant ontology, and biological pathways. Networks and associated evidence of the majority of the currently available data types are visualized in Cytoscape. CORNET is available at https://bioinformatics.psb.ugent.be/cornet.},
  author       = {De Bodt, Stefanie and Inz{\'e}, Dirk},
  booktitle    = {Jasmonate signaling : methods and protocols},
  editor       = {Goossens, Alain and Pauwels, Laurens},
  isbn         = {9781627034135},
  issn         = {1064-3745},
  language     = {eng},
  pages        = {327--343},
  publisher    = {Humana Press},
  series       = {Methods in Molecular Biology},
  title        = {A guide to CORNET for the construction of coexpression and protein-protein interaction networks},
  url          = {http://dx.doi.org/10.1007/978-1-62703-414-2\_26},
  volume       = {1011},
  year         = {2013},
}

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