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TRRD


NAR Molecular Biology Database Collection entry number 49
Kolchanov N.A.1,2, Ananko E.A.1,2, Podkolodnaya O.A.1,2, Ignatieva E.V.1,2, Stepanenko I.L.1,2, Khlebodarova T.M.1,2, Merkulova T.I.1,2, Podkolodny N.L.1,2, Grigorovich D.A.1,2, Poplavsky A.S.1,2, Romashchenko A.G.1,2
1Institute of Cytology & Genetics, SB RAS, Novosibirsk, Russia 2Novosibirsk State University, Novosibirsk, Russia

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 (5'-and 3'- 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://wwwmgs.bionet.nsc.ru/mgs/gnw/trrd/.

Acknowledgements

The work was supported by the RFBR (grants Nos. 02-07-90355, 03-07-90181c, 03-07-90181-b, 03-04-48469-a); grant PCB RAS (No. 10.4); the Siberian Branch of the Russian Academy of Sciences (integration projects Nos. 119); Federal Agency of Science and innovations (grant No. 43.073.1.1.1501); Russian Federal Research Development Program Research and Development in Priority Directions of Science and Technology (contract No. 38/2004); RAS Presidium Programm of Moleculal and Cellular Biology grant, the U.S. Civilian Research and Development Foundation (CRDF) and the Ministry of Education of Russian Federation within the Basic Research and Higher Education Program (NO-008-X1)


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