title: A guide to CORNET for the construction of coexpression and protein-protein interaction networks.
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.
authors.affiliation: Department of Plant Systems Biology, VIB, Gent, Belgium.
authors.forename: Stefanie
authors.initials: S
authors.lastname: De Bodt
authors.forename: Dirk
authors.initials: D
authors.lastname: Inzé
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D029681:Arabidopsis Proteins / Q000235:genetics; D057225:Data Mining; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis; D025941:Protein Interaction Mapping; D060066:Protein Interaction Maps; D057386:Search Engine; D012984:Software; D059467:Transcriptome
chemical_list: D029681:Arabidopsis Proteins