Samsonova M.G., Savostyanova K.G., Serov V.N., Spirov A.V., Surkova S.Yu.
Institute for High Performance Computing and Data Bases, 198005, St.Petersburg, Fontanka 120, office 7, Russia; Fax +7-812-251-8314, E-mail samson@fn.csa.ru
A fundamental activity over the next two decades will involve the analysis
of the integrated structure and behaviour of genetic networks. The accomplishment
of this task will require the development of new theories and algorithms
in mathematics, as well as the development of appropriate databases. The
structure of such databases should be oriented towards the representation
of the results of analysis of genetic network's organization, function,
and evolution. We describe the construction of a prototype of such a database,
called GeNet. GeNet satisfies virtually all of the criteria to genetic
network databases (Samsonova et al., in press) for a selected set of critical
developmental networks. GeNet is located at http://www.csa.ru/Inst/gorb_dep/inbios/genet/genet.htm
and its mirrow site http://www.mssm.edu/molbio/genet/genet.htm.
GeNet is a hypertext database. Different sections of GeNet hold information
on genetic networks in sea urchin, Drosophila and vertebrates. GeNet contains
the maps of the functional connections within the network, the experimental
results from which these connections were inferred, numerical and graphical
data on expression patterns of network genes at different times during
development, theoretical models of genetic networks. User-friendly interface
to GeNet implemented as Java applet enables the user to visualize the organization
of the genetic network and its spatio-temporal behavior, as well as to
simulate the dynamics of signal transduction in the network under Bolean
network model. Besides tools for retrieval and visualization of information
GeNet contains tool which enables the user to construct interactively the
genetic network of interest and to evaluate its dynamics. Three entry points
allow the user to browse the database, to search the database and to work
with genetic network. The current GeNet version holds approximately 900
files in *.html and *.gif format and occupies ca. 10 Mb of disk space.
It contains the information on 250 genes and 70 regulatory elements. GeNet
holds 11 genetic network maps and 50 images of genes expression patterns.