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
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.
Access a random TRRD entries:
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 )