Automatic generation of gene networks schemes from formalized description in the GeneNet database

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).