Welcome to MetNetMetNet is in-development, publicly available software for analysis of genome-wide mRNA, protein, and metabolite profiling data. The software is designed to enable the biologist to visualize, statistically analyze, and model a metabolic and regulatory network map of Arabidopsis, combined with gene expression profiling data.
MetNet will provide a framework for the formulation of testable hypotheses regarding the function of specific genes, and in the long term will provide the basis for identification of metabolic and regulatory networks that control plant composition and development.
new We now have video-tutorials on our site, to quickly get you up to speed!
The MetNet database (MetNetDB) contains integrative information on networks of metabolic and regulatory and interactions in Arabidopsis and Soybean. This information is based on input from biologists in their area of expertise. In addition to the MetNet-curated interactions, we provide Aracyc-curated pathways and AGRIS-curated regulatory network. The data in MetNetDB is updated regularly.
Types of interactions in MetNetDB include transcription, translation, protein modification, assembly, allosteric regulation, translocation from one subcellular compartment to another. Other fields describing the interactions are subcellular location, confidence, directionality, references, evidence, and synonyms. Data on entities (DNA, RNA, polypeptides, protein complexes, metabolites) are derived from web databases (gene related databases: TAIR, GO, MapMan/GabiPD; protein related databases: PPDB, AMPDB, AtNoPDB, AraPerox, PLprot, BRENDA; metabolite related databases: ChEBI, PubChem, KEGG, NCI compound library, NIST MS library), in some cases with additional annotation by experts.
Network information from MetNetDB can be extracted and ported to a variety of applications, such as exploRase, which uses the network in conjunction with statistical analysis of expression data; to Cytoscape/FCM, which finds cycles and pathways in the network, and visualizes and models it in combination with expression data; and to MetNetVR, where the network can be visualized in 3D. XML Builder automatically builds new network XML files from the most current data in MetNetDB. A HiveMind-based service is also under extensive development to provide data in MetNetDB for all other MetNet tools under one integral platform.
The most advanced stage of involvement in MetNet is to contribute your own pathways. Currently efforts are underway to integrate grape pathways into our platform, but other organisms are welcome as well.
In order to become a collaborator, you will need to have or create a MetNet user account. You can then upload pathways either through this website or our custom-built curator application.
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FundingFunding provided by:
National Science Foundation Arabidopsis 2010
MetNet: Integrated Software for Arabidopsis Systems Biology
Wurtele (PI), Berleant, Cook, Dickerson, Miller
Additional support from ISU College of Liberal Arts & Sciences and Plant Sciences Institute
How to cite MetNet?Wurtele ES, Li L, Berleant D, Cook D, Dickerson JA, Ding J, Hofmann H, Lawrence M, Lee EK, Li J, Mentzen W, Miller L, Nikolau BJ, Ransom N, Wang Y, 2007. MetNet: Systems Biology Software for Arabidopsis. In: Concepts in Plant Metabolomics. Springer. pp 145-158.
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