<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <p>MetNet (http://www.botany.iastate.edu/∼mash/metnetex/metabolicnetex.html) is publicly
available software in development for analysis of genome-wide RNA, protein
and metabolite profiling data. The software is designed to enable the biologist to
visualize, statistically analyse and model a metabolic and regulatory network map
of <italic>Arabidopsis</italic>, combined with gene expression profiling data. It contains a JAVA
interface to an interactions database (MetNetDB) containing information on regulatory
and metabolic interactions derived from a combination of web databases (TAIR,
KEGG, BRENDA) and input from biologists in their area of expertise. FCModeler
captures input from MetNetDB in a graphical form. Sub-networks can be identified
and interpreted using simple fuzzy cognitive maps. FCModeler is intended to develop
and evaluate hypotheses, and provide a modelling framework for assessing the large
amounts of data captured by high-throughput gene expression experiments. FCModeler
and MetNetDB are currently being extended to three-dimensional virtual reality
display. The MetNet map, together with gene expression data, can be viewed using
multivariate graphics tools in GGobi linked with the data analytic tools in R. Users
can highlight different parts of the metabolic network and see the relevant expression
data highlighted in other data plots. Multi-dimensional expression data can be
rotated through different dimensions. Statistical analysis can be computed alongside
the visual. MetNet is designed to provide a framework for the formulation of testable
hypotheses regarding the function of specific genes, and in the long term provide
the basis for identification of metabolic and regulatory networks that control plant
composition and development.</p>
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Comp Funct Genomics. 2003 Apr; 4(2):239-245