Information about TRRD

Search in TRRD: Browsing Genes by species

TRRD as a part of GeneExpress

INTRODUCTION

The Transcription Regulatory Regions Database (TRRD) is being developed at the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, since 1993. TRRD is designed for accumulation of experimental data on extended regulatory regions of eukaryotic genes. The TRRD format allows to describe the modular structure of transcription regulatory regions and the hierarchy of theirs constituent regulatory units. The following regulatory units are being considered:

cis-elements providing the interaction of transcription factors with DNA;
composite elements supporting DNA-protein and protein-protein interactions between the neighbouring sites, and the corresponding factors causing either synergistic or antagonistic regulatory effects;
promoters providing formation of the basal transcription complexes;
enhancers and silencers modulating transcription level;
extended transcription regulatory regions located in 5'- and 3'-flanking DNA;
the system of integral regulation of gene transcription.

A database entry corresponds to a single gene.

During the last year, TRRD was considerably improved by introducing a new format of data representation. The TRRD release 4 provides a more complete description of gene expression regulation patterns and the structural peculiarities of regulatory regions so that maximum of information is presented in a computer-readable form.

The TRRD contains five interconnected tables:

TRRDGENES table contains a general information about all the genes described in TRRD and their regulatory units. It is the main table of the database providing linkage with all the other tables.
TRRDSITES table contains the detailed information on transcription factor binding sites. Site description is provided by the references to TRRDGENES, TRRDFACTORS, and TRRDBIB tables of TRRD. In addition, TRRDSITES table is connected to TRANSFAC and EMBL/GenBank databases, as well as to ACTIVITY and SiteRecognition software of the GeneExpress System.
TRRDFACTORS table contains the detailed description of the transcription factors binding to the sites stored in TRRD. Factors contained in TRRDFACTORS table are supplied by the references to theirs description in TRANSFAC database.
TRRDEXP table contains the description of the gene expression patterns. It is supplied with the references to TRRDGENES and TRRDBIB tables as well as to TRRDSITES table offering the information on the sites providing this particular expression pattern.
TRRDBIB table contains the complete bibliographic references of all the papers annotated in TRRD.

CONTENT OF THE CURRENT RELEASE

The genes contained in TRRD could be classified into groups according to species specificity, type of a protein encoded by the gene, and the functional role of a gene.

The genes described in TRRD refer to different eukaryotic species: human (39.7%), mouse (25.1%), rat (16%), chicken (6%), hamster (1.2%), and others (4.3%). This release contains also an information on transcription regulatory regions in plants (7.7%) that lacks in the previous releases.

Several functionally important gene systems are described in TRRD: interferon-inducible genes, erythroid-specific regulated genes, genes of lipid metabolism, glucocorticoid-controlled genes, cell cycle-dependent genes, endocrine system genes, heat shock genes, and plant genes.

TRRD contains the information on genes encoding proteins with a wide variety of functions. According to EPD database classification, TRRD is subdivided into several groups: genes encoding structural proteins (16%), storage and transport proteins (20%), enzymes (19%), regulatory proteins, including hormones, growth factors, etc. (20%), proteins related to stress or pathogen defence reactions (10%), and others (15%).

FUTURE PROSPECTS

The following extensions of TRRD are planned in future. First, the format of experimental data presentation in TRRD will be improved. In particular, the novel formats will be developed for description of interaction of transcription factors to basal transcription machinery, the influence of nucleosomal chromatin organization, methylation, and mutations on transcription regulation. Second, we intend to start the integration of TRRD with a variety of other molecular biological databases available via Internet using CORBA technique. We plan to continue integration of TRRD with various software for analysis and recognition of regulatory genomic sequences within the framework of GeneExpress system. Finally, we plan to continue the expansion of TRRD with the new experimental data on transcription regulation, making the especial emphasis to the genes controlling hematopoiesis, stress response, and functioning of nervous, endocrine, and immune systems.