Trrd: a Database on Experimentally Identified Transcription Regulatory Regions and Transcription Factor Binding Sites

Abstract

Motivation: The main goal of TRRD (Transcription Regulatory Regions Database) development is the most complete and adequate description of the structural and functional organization of transcription regulatory gene regions in eukaryotes based on the data obtained experimentally. Results: The overall information contained in the current TRRD release is represented as eight libraries: TRRDGENES, TRRDUNITS, TRRDEXP, TRRDSITES, TRRDFACTORS, TRRDLCR, TRRDSTARTS, and TRRDBIB. TRRD compiles the data on 2344 genes, 14 407 patterns of their expression, 3490 regulatory units, and 10 135 transcription factor binding sites associated with them. This database contains only experimentally confirmed information. TRRD is filled in by manual annotation of scientific publications. The data incorporated into TRRD is a result of annotation of 7609 scientific papers. The main tool for searching TRRD and navigation in it is SRS. A large number of indexed fields in the SRS version of TRRD allow the user to generate complex queries both within individual libraries and involving several libraries. TRRD has thesauruses that provide additional options for data access. The number of databases linked to TRRD has been increased. Availability: http://www.bionet.nsc.ru/trrd/.

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Cite this paper

@inproceedings{Kolchanov2008TrrdAD, title={Trrd: a Database on Experimentally Identified Transcription Regulatory Regions and Transcription Factor Binding Sites}, author={Nikolay A. Kolchanov and Olga A. Podkolodnaya and Ananko E A and Ignatieva E V and Stepanenko I L and Khlebodarova T M and Merkulov V M and Merkulova T I and Podkolodny N L and Romashenko A G}, year={2008} }