About CORNET 2.0 for Arabidopsis (Please use Firefox - see FAQ)
Linking different components of a system by constructing CORrelation NETworks.
TOOLS AND FUNCTIONALITIES:
The co-expression tool calculates the correlation between gene expression profiles using one or more precompiled expression datasets and as such identifies possible functional associations between genes.
The PPI tool interrogates available protein-protein interaction databases (both experimental and predicted interactions) and the AraNet probabilistic fucntional gene network.
The TF tool retrieves regulatory interactions from AGRIS and inferred from CORNET microarray data (genetic_modification_design).
Integrate different data types by subsequently running the different tools. For instance integrate co-expression and protein-protein interactions: Start with the co-expression tool and continue on to the PPI tool or vice versa. These options can be selected on the bottom of the page.
Functional information on the genes in the constructed network are retrieved (localisation, TAIR functional descriptions, Gene Ontology, Plant Ontology, MapMan pathways and processes, protein domains, PubMed IDs and phenotypes). Link out to other external databases by right-clicking the nodes in Cytoscape.
Browse experiments allows you to search the microarray experiments in the CORNET database using ontologies, download raw data and preprocessed data that can be used at a later time in CORNET or in other software.
Upload/Edit allows you to upload your personal microarray experiments into the CORNET system. After uploading, these experiments will be available through Browse experiments. (data is stored for 1 day - see FAQ for details)
CORNET is developed by the Department of Plant Systems Biology, VIB UGent (Belgium). Questions and remarks can be addressed to firstname.lastname@example.org. You can also have a look at our Frequently Asked Questions. Please cite: De Bodt et al. (2010) Plant Phys 152:1167-1179, De Bodt et al. (2012) New Phytol. 195:707-720.