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CORNET 2.0: integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations

Stefanie De Bodt (UGent) , Jens Hollunder (UGent) , Hilde Nelissen (UGent) , Nick Meulemeester and Dirk Inzé (UGent)
(2012) NEW PHYTOLOGIST. 195(3). p.707-720
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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, named CORNET. This tool allows the browsing of microarray data, the construction of coexpression and proteinprotein interaction (PPI) networks and the exploration of diverse functional annotations. Here, we present the new functionalities of CORNET 2.0 for data integration in plants. First of all, CORNET allows the integration of regulatory interaction datasets accessible through the new transcription factor (TF) tool that can be used in combination with the coexpression tool or the PPI tool. In addition, we have extended the PPI tool to enable the analysis of genegene associations from AraNet as well as newly identified PPIs. Different search options are implemented to enable the construction of networks centered around multiple input genes or proteins. New functional annotation resources are included to retrieve relevant literature, phenotypes, plant ontology and biological pathways. We have also extended CORNET to attain the construction of coexpression and PPI networks in the crop species maize. Networks and associated evidence of the majority of currently available data types are visualized in Cytoscape.
Keywords
RESOURCE, NETWORKS, TOOL, SYSTEMS-BIOLOGY, HYPOTHESIS GENERATION, ATTED-II, EXPRESSION, ARABIDOPSIS-THALIANA, MOLECULAR INTERACTION DATABASE, PROBE LEVEL DATA, networks, maize, data integration, CORNET, bioinformatics, Arabidopsis

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Citation

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Chicago
De Bodt, Stefanie, Jens Hollunder, Hilde Nelissen, Nick Meulemeester, and Dirk Inzé. 2012. “CORNET 2.0: Integrating Plant Coexpression, Protein-protein Interactions, Regulatory Interactions, Gene Associations and Functional Annotations.” New Phytologist 195 (3): 707–720.
APA
De Bodt, Stefanie, Hollunder, J., Nelissen, H., Meulemeester, N., & Inzé, D. (2012). CORNET 2.0: integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations. NEW PHYTOLOGIST, 195(3), 707–720.
Vancouver
1.
De Bodt S, Hollunder J, Nelissen H, Meulemeester N, Inzé D. CORNET 2.0: integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations. NEW PHYTOLOGIST. 2012;195(3):707–20.
MLA
De Bodt, Stefanie, Jens Hollunder, Hilde Nelissen, et al. “CORNET 2.0: Integrating Plant Coexpression, Protein-protein Interactions, Regulatory Interactions, Gene Associations and Functional Annotations.” NEW PHYTOLOGIST 195.3 (2012): 707–720. Print.
@article{2973988,
  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, named CORNET. This tool allows the browsing of microarray data, the construction of coexpression and proteinprotein interaction (PPI) networks and the exploration of diverse functional annotations. Here, we present the new functionalities of CORNET 2.0 for data integration in plants. First of all, CORNET allows the integration of regulatory interaction datasets accessible through the new transcription factor (TF) tool that can be used in combination with the coexpression tool or the PPI tool. In addition, we have extended the PPI tool to enable the analysis of genegene associations from AraNet as well as newly identified PPIs. Different search options are implemented to enable the construction of networks centered around multiple input genes or proteins. New functional annotation resources are included to retrieve relevant literature, phenotypes, plant ontology and biological pathways. We have also extended CORNET to attain the construction of coexpression and PPI networks in the crop species maize. Networks and associated evidence of the majority of currently available data types are visualized in Cytoscape.},
  author       = {De Bodt, Stefanie and Hollunder, Jens and Nelissen, Hilde and Meulemeester, Nick and Inz{\'e}, Dirk},
  issn         = {0028-646X},
  journal      = {NEW PHYTOLOGIST},
  keyword      = {RESOURCE,NETWORKS,TOOL,SYSTEMS-BIOLOGY,HYPOTHESIS GENERATION,ATTED-II,EXPRESSION,ARABIDOPSIS-THALIANA,MOLECULAR INTERACTION DATABASE,PROBE LEVEL DATA,networks,maize,data integration,CORNET,bioinformatics,Arabidopsis},
  language     = {eng},
  number       = {3},
  pages        = {707--720},
  title        = {CORNET 2.0: integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations},
  url          = {http://dx.doi.org/10.1111/j.1469-8137.2012.04184.x},
  volume       = {195},
  year         = {2012},
}

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