CORNET 2.0: integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations.
To enable easy access and interpretation of heterogeneous 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 protein-protein 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 gene-gene 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. CORNET is available at https://bioinformatics.psb.ugent.be/cornet.
Department of Plant Systems Biology, Flanders Institute for Biotechnology, and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
Stefanie
S
De Bodt
Department of Plant Systems Biology, Flanders Institute for Biotechnology, and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
Jens
J
Hollunder
Department of Plant Systems Biology, Flanders Institute for Biotechnology, and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
Hilde
H
Nelissen
Department of Plant Systems Biology, Flanders Institute for Biotechnology, and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
Nick
N
Meulemeester
Department of Plant Systems Biology, Flanders Institute for Biotechnology, and Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
Dirk
D
Inzé
D017360:Arabidopsis / Q000737:chemistry / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D056726:Genetic Association Studies / Q000379:methods; D020407:Internet; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D025941:Protein Interaction Mapping / Q000379:methods; D060066:Protein Interaction Maps; D014157:Transcription Factors / Q000235:genetics; D014584:User-Computer Interface; D003313:Zea mays / Q000737:chemistry / Q000235:genetics
D029681:Arabidopsis Proteins; D014157:Transcription Factors