GeNet, the database of genetic networks

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.

  1. G. Samsonova, K.G.Savostyanova, V. N.Serov, A. V.Spirov.
  2. I.V.Tretyakova The GeNet database. Bioinformatics, submitted