Nuclc. Acids. Res. OUP
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH ARTICLES TABLE OF CONTENTS
Compilation Paper
Categories List
Alphabetical List
Search Summary Papers

TRRD

http://www.bionet.nsc.ru/trrd/

Contact   kol@bionet.nsc.ru


Database Description

Transcription Regulatory Regions Database (TRRD) is an informational resource containing an integrated description of the gene transcription regulation. Each TRRD entry corresponds to a particular gene and contains descriptions of several hierarchical levels of transcription regulation, including (1) transcription factor binding sites, (2) regulatory units (promoters, enhancers, and silencers), (3) regulatory regions (3-and 5- regulatory regions, exons, and introns), and (4) locus control regions. Description of each regulatory level may contain both its structural characteristics (sequence, localization, etc.) and functional properties (effect on transcription activity of a gene; cell type, tissue, or organ specificity; cell-cycle phase or ontogenetic stage specificity, etc.). In the database, the data on LCR, regulatory regions, regulatory units, and transcription factor binding sites are supplemented with (1) descriptions of transcription factors used in the experiments on either binding capacities or functional activities of the corresponding sites, (2) patterns of gene expression regulation, and (3) references to original publications. All the data are distributed between seven following databases: TRRDGENES (general gene description), TRRDLCR (locus control regions); TRRDUNITS (regulatory regions: promoters, enhancers, silencers, etc.), TRRDSITES (transcription factor binding sites), TRRDFACTORS (transcription factors), TRRDEXP (expression patterns), and TRRDBIB (experimental publications). TRRD is regularly updated in accordance with new experimental evidence. All the information is inputted into the database by experts in biology basing on analysis and annotation of papers reporting experimental data. Each type of experiment is designated with specific digital code, indicated in the fields 'ExperimentCodes' of the databases TRRDGENES, TRRDSITES, and TRRDUNITS. Sequence Retrieval System (SRS) is used as a basic tool for navigating and searching TRRD and integrating it with external informational and software resources. The visualization tool, TRRD Viewer, provides the information representation in a form of maps of gene regulatory regions. The option allowing nucleotide sequences to be searched for according to their homology using BLAST is also included. TRRD is available at http://www.bionet.nsc.ru/trrd/

Category   Gene Identification and Structure

Go to the abstract in the NAR 2002 Database Issue.

 

Compilation Paper
Categories List
Alphabetical List
Search Summary Papers