Ananko E. A., Kolpakov F. A., Kolesov G. B., Kolchanov N. A.
Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, 630090, Novosibirsk, Russia; FAX: 7-(3832)331278; E-mail: eananko@bionet.nsc.ru
Gene networks - gene ensembles functioning in a coordinated manner -
play a key role in regulation of physiological functions in eukaryotic
organisms. One of the major tasks of molecular biology is to gain the insight
into fine mechanisms of these regulatory processes. The GeneNet database
is designed for accumulation of the formalized description of gene networks
and signal transduction pathways. Antiviral response and erythropoiesis
regulation were used as examples to try out the basic principles of the
formalized gene network description and integration of the data obtained
in different organisms into a unified scheme. The object-oriented approach
was used to divide all the gene network components into entities (any material
objects) and relations between the entities. Four classes of entities are
distinguished: (1) Cell (tissue, organ); (2) Protein; (3) Gene; and (4)
Substance. Provision is made for addition of new object types if necessary.
Each type of objects is described in a separate table. Relations between
the objects are described in a separate table too and grouped into two
basic types: reactions and regulatory events. The three following hierarchical
levels are considered as a first approximation to the description of the
gene network: (1) organism level. (2) single cell level, and (3) single
gene level. A Java applet (GeneNet Viewer) for automatic generation of
the gene network diagrams from the textual information contained in the
GeneNet database was developed. GeneNet is supplemented with a system of
filters providing the sorting of the gene network components by organism
species, cell type, and inducer. GeneNet viewer is provided with the tools
for data navigation including interactive images on the diagram, on-line
help, interactive cross-references within the GeneNet database, references
to the EMBL, SWISSPROT, TRANSFAC, MEDLINE, and linkages to the TRRD database.
GeneNet is available via the Internet at http://promot.bionet.nsc.ru/
through the SRS system (http://sgi.sscc.ru).