MetNet Plug-ins for Cytoscape are a set of Java open-source programs for visualizing and analyzing biological networks A tool for plotting and analyzing large sets of data while using as little memory as possible Graphical Java interface for MetNetDB. Used to both query and modify the database Exploratory multivariate analysis of Systems Biology data Map experimental data to different cell compartments, pathways, and GO Ontology categories in order to give a "bird's eye view" of the data Integrate the MetNet tools and MetNetDB into a single platform Not yet available Not yet available Virtual reality software for exploring cellular metabolism Different ways to consume MetNet datasources SOAP-based interface to MetNet Stand-alone Java™ program that helps biologists and medical workers get the most out of PubMed search Plant-based tool to explore literature, and to annotate metabolic and regulatory interactions and biomolecules

Welcome to MetNet

MetNet 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!

Pathway of the day

Selected pathway: traumatin and (Z)-3-hexen-1-yl acetate biosynthesis

Entities of the day

Gene of the day: AT1G09940 / Glutamyl-tRNA reductase family protein
This gene participates in 4 pathways: Chlorophyll Biosynthesis (WYJ) - heme biosynthesis I - superpathway of proto- and siroheme biosynthesis - tetrapyrrole biosynthesis I -

Metabolite of the day: glycerate
This metabolite participates in 1 pathways: C2 Photorespiration cycle (WYJ) -



Explore Analyze Contribute
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.


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You can browse pathways either by organelle or by classification

MetNet tools

exploRase
MetaOmGraph
atGeneSearch
MetNetAPI
More tools...

Funding

Funding provided by:


National Science Foundation Arabidopsis 2010
MetNet: Integrated Software for Arabidopsis Systems Biology
Wurtele (PI), Berleant, Cook, Dickerson, Miller
DBI-0520267 (9/2005-9/2008)

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.

Copyright © 2006-2013 Wurtele lab. Copyright refers to the integration and online application, not the data from the various sources.

 

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