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TRRD Frequently Asked Questions (FAQ)

1. What is the TRRD database?
2. What for the TRRD could be applied?
3. What are the features discriminating TRRD database from the other databases on DNA sequence motifs?
4. Where has TRRD database been developed?
5. How is the access to TRRD provided via the WWW?
6. Is TRRD freely accessible for users?
7. Is it possible to obtain a flat-file?
8. What is the source of data accumulated in TRRD?
9. What are the ways of searching ?
10. How to get an information about the genes of particular organism?
11. How to extract information about the genes that are expressed in particular organ, for example, liver?
12. How to obtain information about the genes that are induced (or regulated) under definite stimuli (external stimuli) ?
13. Is it possible to create a set of sequences of extensive regulatory regions (e.g., promoters) using the TRRD database?
14. Is it possible to determine if a nucleotide sequence of interest is homologous to the site(s) stored in the TRRD database?

 

1. What is the TRRD database?

Transcription Regulatory Regions Database (TRRD) is developed for accumulation of experimental information on the structure-function features of regulatory regions of eukaryotic genes. Each entry of TRRD corresponds to a particular gene. The annotated part of an entry includes the structure-function description of gene regulatory regions composed by regulatory units (promoters, silencers, enhancers, etc.), individual transcription factor binding sites that constitute these regulatory units, and transcription factors that bind to these sites. In addition, the entry contains the gene expression patterns and references to original publications.

2. What for the TRRD could be applied?

The TRRD database has been developed to provide the research on mechanisms controlling eukaryotic gene expression on the transcriptional level. The experimental data concerning various features of gene expression regulation, gene classifications, structure of the gene regulatory regions, promoters, silencers and enhancers, transcription factor binding sites are stored in the database.

3. What are the features discriminating TRRD database from the other databases on DNA sequence motifs?

The TRRD gives a representation on integral transcription regulation system of the eukaryotic genes. The format used in TRRD is based on the model of module-hierarchic organization of transcription regulatory regions of eukaryotic genes. According to this model, the lowest level of regulatory region organization corresponds to transcription factor binding sites; the next level, to regulatory units ( promoters, enhancers, silencers). The regulatory units listed above are components of transcription regulatory regions that represent the next hierarchic regulatory level and are located in 5- and 3- gene flanking regions and in introns. Description of a regulatory element of each level in addition to structure characteristics (elements location and nucleotide sequence) may be supplemented with its functional features (effect on gene transcription activity, tissue- and stage-specificities, etc). Thus, the TRRD database allows both the structural and functional features regulatory elements from each level.
One more essential discrepancy of TRRD differentiating it from the other databases is the complex approach to a gene description. In addition to the structural and functional feathers of the gene transcription regulatory regions, the experimental data on gene expression patterns may be stored in the TRRD format. The link between the table TRRDEXP (gene expression patterns) and the table TRRDSITES (transcription factor binding sites) provides possibility to document the results on the experiments revealing the role of particular regulatory units or transcription factor binding sites in realization of gene expression pattern given.

4. Where has TRRD database been developed?

The TRRD database is being developed at the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, since 1993. The scientific supervisor of TRRD Professor Nikolay A. Kolchanov, Head of Laboratory of Theoretical Genetics can be contacted by e-mail kol@bionet.nsc.ru

5. How is the access to TRRD provided via the WWW?

TRRD release 4.*.* with limited options is available by URL http://wwwmgs.bionet.nsc.ru/mgs/dbases/trrd4/
The TRRD is also accessible via the mirror sites at http://www.cbil.upenn.edu/mgs/ (the University of Pennsylvania, USA) and http://pcbsd.nihs.go.jp/mgs/ (the National Institute of Health Sciences, Japan)

6. Is TRRD freely accessible for users?

TRRD database is a commercial product. To purchase this product, it is necessary to enter the licence agreement. The demo version with limited options is Internet-available at http://wwwmgs.bionet.nsc.ru/mgs/dbases/trrd4/ and mirror sites. The commercial product is delivered on the basis of the non-exclusive licence agreement limited by duration of a year or more. Conditions of an agreement are fixed with the user. In order to set a contract, please, apply to the TRRD scientific supervisor Nikolay A. Kolchanov by e-mail kol@bionet.nsc.ru or by Fax +7-3832-331278.

7. Is it possible to obtain a flat-file?

Terms of receiving a flat-file should be agreed by the contract or the licence agreement. For entering the contract, please, address to the TRRD scientific supervisor Nikolay A. Kolchanov by e-mail kol@bionet.nsc.ru or by Fax +7-3832-331278.

8. What is the source of data accumulated in TRRD?

To input the information into the database, experts in biology annotate publications on the relevant experimental data. For example, the data for TRRD release 4.3.4 which comprised the description of 961 genes, 4523 transcription factor binding sites, 1355 regulatory units, were accumulated through annotating 3170 scientific publications. The descriptions of transcription factor binding site are based on the results of such experimental procedures as DNase I footprinting, gel-mobility shift assay and transient expression analysis. The descriptions of gene expression patterns are based on results of Northern and Western blotting, nuclear run-off, RT/PCR analyses, etc. Special lines from TRRDSITES table contain the digital codes of experiments and the names of cells and cell lines used in experiments.

9. What are the ways of searching ?

TRRD can be searched on the Internet with the Sequence Retrieval System (SRS). Implementation in SRS distributes the contents of the TRRD flat file corresponding to an entry between six cross-linked tables: TRRDGENES (general description of genes), TRRDEXP (description of the gene expression patterns), TRRDUNITS (description of regulatory units  -promoters, enhancers, silencers), TRRDSITES (description of transcription factor binding sites), TRRDFACTORS (description of transcription factors), and TRRDBIB  (references). Such distribution represents the information on transcription regulation of each gene in a convenient manner. At present more than 80 types of lines from TRRD entry are indexed providing effective search with SRS.
Provision is made for the other ways of navigating through TRRD database, including possibilities  of Blast search and the browsing system.
While developing TRRD, the main attention was focused on description of genes within functional systems. The information on these gene groups can be obtained from TRRD sections.

10. How to get an information about the genes of particular organism?

It is possible (i) to browse TRRD by ordering the species specificity and (ii) by means of the SRS system. Choose the table TRRDGENES and make the search by the line OS (Species), by inserting as a keyword the name of an organism or the species name in Latin.

11. How to extract information about the genes that are expressed in particular organ, for example, liver?

It is possible to do this by the SRS. Choose the table TRRDEXP and organise the combined search with "BUTNOT", by inserting the keyword "liver" in the line RO (Organ), and the keyword "none" and "undetectable" in the line RL (Level). As a result, the gene expression patterns will be extracted. The information about genes may be obtained using the link to the table TRRDGENES.

12. How to obtain information about the genes that are induced (or regulated) under definite stimuli (external stimuli) ?

By using the SRS. Choose the table TRRDEXP and perform the combined search with "BUTNOT", by inserting the name of an inductor as a keyword in the field RI (Inductor/Repressor) and the word "no effect" in the field FF (Influence). The information about the genes may be obtained using the link to the table TRRDGENES.

13. Is it possible to create a set of sequences of extensive regulatory regions (e.g., promoters) using the TRRD database?

The sequences of regulatory regions of genes can be extracted from the table TRRDUNITS.

14. Is it possible to determine if a nucleotide sequence of interest is homologous to the site(s) stored in the TRRD database?

The search for the regions of an arbitrary nucleotide sequence that are homologous to transcription factor binding sites described in the TRRD database should be performed by applying the software program RegScan.

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