Gene networks: formalized description and visualization in the GeneNet database

Ananko E.A., Kolpakov F.A., Podkolodnaya O.A., Ignatieva E.V., Goryachkovsky T.N.,Stepanenko I.L., Busygina T.V., Kolesov G.B., Grigorovich D.A., Kolchanov N.A.

Proc. of the international conference on Theory and Mathematics in Biology and Medicine. 1999. Amsterdam. The Netherlands, June 29 July 3. P. 58-59

Gene networks provide the regulation of physiological processes in eukaryotic organisms. Rapidly increasing information regarding the regulation of gene expression and signal transduction pathways is hard to formalize and systematize. A technology of the formalized description of gene networks in the database GeneNet was developed, which allowed to accumulate information on elementary structures, events and processes. Current version of the database contains the information on the four gene networks regulating antiviral response, lipid metabolism, erythrocyte differentiation and nitrogen fixation in legumes. Also the Java applet was developed. It allows to visualize information from the database GeneNet on three following hierarchic levels: a whole organism, an individual cell and a single gene. GeneNet is available at