Gene networks: a database and its automated visualization through the Internet in the GeneNet computing system

Ananko E.A., Kolpakov F.A., Kolesov G.B.,  Kolchanov N.A.

Proc. I Intern. Conference on Bioinformatics of Genome Regulation and Structure (BGRS'98).
Novosibirsk. Russia. 1998. P. 82-85.

Gene networks provide the regulation of physiological processes in eukaryotic organisms. Ways and means for automated visualization of the gene networks based on their formalized description are needed. Rapidly increasing information regarding the regulation of gene expression and signal transduction pathways is hard to formalize and systematize. The main principles of a formalized description of various regulatory processes have been worked out for the GeneNet computer system designed for accumulation of the data on gene networks and their visualization through the Internet. The GeneNet system is bipartite and includes: (1) a database containing information on gene networks and (2) a Java program for automated construction of the gene network diagrams based on their formalized description in the database. The GeneNet graphical user interface allows visualization and exploration of the GeneNet database through the Internet. The GeneNet is a part of GeneExpress - an intellectual system for analysis of genomic regulatory sequences (http://wwwmgs.bionet.nsc.ru/mgs/systems/geneexpress/), developed in the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences. GeneNet is available at http://wwwmgs.bionet.nsc.ru/mgs/systems/genenet/.