ABSTRACT
A database for gene networks GeneNet was created. The main principles of formalized description of gene networks for the cases of regulation of antiviral responses and hemopoiesis were developed. A program for automatic graphical representation of diagrams of gene networks was created, which is based on their formalized description. A system of filters was developed, which makes it possible to select individual network components for graphical representation. The selection can be performed with respect to specific type of treatment, species, and/or cell type. The GeneNet database is accessible via Internet at http://wwwmgs.bionet.nsc.ru/systems/MGL/Gen eNet.
Subject(s)
Computer Graphics , Databases, Factual , Animals , Automation , Base Sequence , Hematopoiesis , Humans , Mice , Virus Diseases/immunologyABSTRACT
GeneExpress system has been designed to integrate description, analysis, and recognition of eukaryotic regulatory sequences. The system includes 5 basic units: (1) GeneNet contains an object-oriented database for accumulation of data on gene networks and signal transduction pathways and a Java-based viewer that allows an exploration and visualization of the GeneNet information; (2) Transcription Regulation combines the database on transcription regulatory regions of eukaryotic genes (TRRD) and TRRD Viewer; (3) Transcription Factor Binding Site Recognition contains a compilation of transcription factor binding sites (TFBSC) and programs for their analysis and recognition; (4) mRNA Translation is designed for analysis of structural and contextual features of mRNA 5'UTRs and prediction of their translation efficiency; and (5) ACTIVITY is the module for analysis and site activity prediction of a given nucleotide sequence. Integration of the databases in the GeneExpress is based on the Sequence Retrieval System (SRS) created in the European Bioinformatics Institute.
Subject(s)
Computer Systems , Genes, Regulator , Genome , Artificial Intelligence , Binding Sites , Databases, Factual , Eukaryotic Cells , Gene Expression Regulation , Protein Biosynthesis , RNA, Messenger/genetics , Software , Transcription Factors/genetics , Transcription Factors/metabolism , Transcription, GeneticABSTRACT
MOTIVATION: Gene networks that provide the regulation of physiological processes are the basic feature of organisms. Information regarding the regulation of gene expression and signal transduction pathways is increasing rapidly. However, the information is hard to formalize and systematize. Ways and means for automated visualization of the gene networks based on their formalized description are needed. RESULTS: The object-oriented database GeneNet and the software for its automated visualization have been developed. The main principles of a formalized description of the gene network have been worked out. Antiviral response and erythropoiesis are provided as examples to show how this is achieved. The GeneNet graphical user interface written in Java provides automated generation of the gene network diagrams and allows visualization and exploration of the GeneNet database through the Internet. A system of filters allows the selection of particular components of the network for visualization. AVAILABILITY: The GeneNet database and its graphical user interface are available at http://wwwmgs.bionet.nsc.ru/systems/MGL/GeneN et/ CONTACT: fedor@bionet.nsc.ru
