Bioinformatics, Vol 15, 669-686, Copyright © 1999 by Oxford University Press
NA Kolchanov, MP Ponomarenko, AS Frolov, EA Ananko, FA Kolpakov, EV Ignatieva, OA Podkolodnaya, TN Goryachkovskaya, IL Stepanenko, TI Merkulova, VV Babenko, YV Ponomarenko, AV Kochetov, NL Podkolodny, DV Vorobiev, SV Lavryushev, DA Grigorovich, YV Kondrakhin, L Milanesi, E Wingender, V Solovyev and GC Overton
MOTIVATION: The goal of the work was to develop a WWW-oriented computer
system providing a maximal integration of informational and software
resources on the regulation of gene expression and navigation through them.
Rapid growth of the variety and volume of information accumulated in the
databases on regulation of gene expression necessarily requires the
development of computer systems for automated discovery of the knowledge
that can be further used for analysis of regulatory genomic sequences.
RESULTS: The GeneExpress system developed includes the following major
informational and software modules: (1) Transcription Regulation (TRRD)
module, which contains the databases on transcription regulatory regions of
eukaryotic genes and TRRD Viewer for data visualization; (2) Site Activity
Prediction (ACTIVITY), the module for analysis of functional site activity
and its prediction; (3) Site Recognition module, which comprises (a)
B-DNA-VIDEO system for detecting the conformational and physicochemical
properties of DNA sites significant for their recognition, (b) Consensus
and Weight Matrices (ConsFrec) and (c) Transcription Factor Binding Sites
Recognition (TFBSR) systems for detecting conservative contextual regions
of functional sites and their recognition; (4) Gene Networks (GeneNet),
which contains an object-oriented database accumulating the data on gene
networks and signal transduction pathways, and the Java- based Viewer for
exploration and visualization of the GeneNet information; (5) mRNA
Translation (Leader mRNA), designed to analyze structural and contextual
properties of mRNA 5'-untranslated regions (5'-UTRs) and predict their
translation efficiency; (6) other program modules designed to study the
structure-function organization of regulatory genomic sequences and
regulatory proteins. AVAILABILITY: GeneExpress is available at
http://wwwmgs.bionet.nsc. ru/systems/GeneExpress/ and the links to the
mirror site(s) can be found at
http://wwwmgs.bionet.nsc.ru/mgs/links/mirrors.html+ ++.
ARTICLES
Integrated databases and computer systems for studying eukaryotic gene expression
Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva 10, Novosibirsk 630090, Russia. kol@bionet.nsc.ru
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