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Information contents

Database schema

General principles
TRRD entry structure
The source of data accumulated in TRRD and digital codes of experiments

General principles

TRRD is designed for accumulation of experimental data on extended transcription regulatory regions of eukaryotic genes. Eukaryotic gene transcription regulation is provided by complex interactions between transcription factors binding specifically to DNA and basal transcription complexes formed near the transcription start site.

The format used in TRRD is based on the model of module-hierarchic organization of transcription regulatory regions of eukaryotic genes. 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).

Example:

structure-functional organization of the human apolipoprotein B gene

TRRD entry structure

An entry of TRRD is a 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.
Implementation in SRS distributes the contents of the TRRD flat file corresponding to an entry between six cross-linked tables presented in the Table 1

Table 1.

Table name The type of data described in the table Data format
TRRDGENES General description of genes

TRRDEXP Gene expression patterns

TRRDUNITS Regulatory Units (promoters, enhancers, silencers)

TRRDSITES Transcription factor binding sites

TRRDFACTORS Transcription factors

TRRDBIB References

Access a random TRRD entries:

  1. human apolipoprotein AI gene (A00264)
  2. human apolipoprotein B gene (A00149)
  3. mouse glutathione peroxidase gene (A00463)
  4. human interferon-beta gene (A00274)

The source of data accumulated in TRRD and digital codes of experiments.

To input the information into the database, experts in biology annotate publications on the relevant experimental data. The list of top twenty annotated journals is presented on the page TRRD statistics.

The descriptions of gene expression patterns are based on results of Northern and Western blotting, nuclear run-off, RT/PCR analyses, etc. The descriptions of transcription factor binding sites are based on the results of such experimental procedures as DNase I footprinting, gel-mobility shift assay and transient expression analysis. The names of cells and cell lines used in experiments and digital codes of experiments are registered in the AG line (table TRRDSITES )

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