title: Integrated databases and computer systems for studying eukaryotic gene expression.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  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+ ++.
authors.affiliation: Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva 10, Novosibirsk 630090, Russia. kol@bionet.nsc.ru
authors.forename: N A
authors.initials: NA
authors.lastname: Kolchanov
authors.forename: M P
authors.initials: MP
authors.lastname: Ponomarenko
authors.forename: A S
authors.initials: AS
authors.lastname: Frolov
authors.forename: E A
authors.initials: EA
authors.lastname: Ananko
authors.forename: F A
authors.initials: FA
authors.lastname: Kolpakov
authors.forename: E V
authors.initials: EV
authors.lastname: Ignatieva
authors.forename: O A
authors.initials: OA
authors.lastname: Podkolodnaya
authors.forename: T N
authors.initials: TN
authors.lastname: Goryachkovskaya
authors.forename: I L
authors.initials: IL
authors.lastname: Stepanenko
authors.forename: T I
authors.initials: TI
authors.lastname: Merkulova
authors.forename: V V
authors.initials: VV
authors.lastname: Babenko
authors.forename: Y V
authors.initials: YV
authors.lastname: Ponomarenko
authors.forename: A V
authors.initials: AV
authors.lastname: Kochetov
authors.forename: N L
authors.initials: NL
authors.lastname: Podkolodny
authors.forename: D V
authors.initials: DV
authors.lastname: Vorobiev
authors.forename: S V
authors.initials: SV
authors.lastname: Lavryushev
authors.forename: D A
authors.initials: DA
authors.lastname: Grigorovich
authors.forename: Y V
authors.initials: YV
authors.lastname: Kondrakhin
authors.forename: L
authors.initials: L
authors.lastname: Milanesi
authors.forename: E
authors.initials: E
authors.lastname: Wingender
authors.forename: V
authors.initials: V
authors.lastname: Solovyev
authors.forename: G C
authors.initials: GC
authors.lastname: Overton
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003199:Computer Systems; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016208:Databases, Factual; D005057:Eukaryotic Cells; D015870:Gene Expression; D020407:Internet; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000235:genetics; D012984:Software; D016385:TATA Box; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D012333:RNA, Messenger; D014157:Transcription Factors; D004247:DNA