General information

How to cite TRRD?

TRRD publications

The latest report on TRRD

Acknowledgments

User's guide

Database schema

How to search TRRD?

Integration with other databases

How is TRRD updated ?

Standardization of information input

TRRD progress (from 1996)

Current TRRD release

TRRD statistics

Information contents

What's new?

The history of changes, improvements and new features

(To view the dynamics of TRRD progress, please, click here)

September 2005

TRRD Release 7.0 on-line

1) New table TRRDSTARTS was introduced. This library compiles the data on the experimentally determined transcription start sites of genes. TRRDSTART contains absolute genome coordinates of the major and minor transcription starts of genes (with indication of the chromosome and release of the genomic database). From this library, it is possible to get the information about specificity

January 2005

New sections were introduced:
"B-TRRD" - Genes Expressed in B cells
"HCV-TRRD" - Hepatitis C Virus–Induced Genes
"EBV-TRRD" - Genes Related to EBV Infection and EBV Transformation
"CLOCK-TRRD" - Genes, controlling circadian rhythm, and genes with circadian expression

March 2004

Additional specialized search system based on hierarchically organized vocabulary on transcription factors is available:
-search for genes or sites regulated by the definite transcription factor.

January 2003

Special search software based on hierarchically organized controlled vocabularies and thesauri was developed.
Specialized search systems, developed for TRRD maintain:
1) search for genes induced (or repressed) by influence of external stimulus;
2) search for genes expressed in specified organ, or tissue, or cells, or stage of organism development;
3) combined search for genes expressed in specified tissue, organ, cells under induction of the specified external stimulus (simultaneously).

December 2002

TRRD Release 6.2 on-line

2) The format was slightly modified. New field was introduced into the table TRRDSITES:

PreferredName (NP), [=preferred names] to compile the information on the standard site name

June 2002

TRRD Release 6.1 on-line

New sections were introduced:
"EP-TRRD" -Genes Expressed in Endocrine Pancreas
"MG-TRRD" - Macrophage-Expressed Genes
"Apoptosis -TRRD" - Apoptosis Genes
"BCF-TRRD" - Genes, controlling blood coagulation and fibrinolysis

May 2002

Thesaurus on organs and tissues in mammals is available.
The specialized browser system based of thesaurus and the SRS technology was developed. The system enables to bring out the list of genes that are expressed in the tissue or organ of a user’s interest.

September 2001

TRRD Release 6.0 on-line

1) New table TRRDLCR was introduced. Each entry of TRRDLCR describes an individual locus control region (LCR), containing the data on the structure of the regulated gene locus, structure of the LCR itself, and the functional characterization of its elements.

2) The format was slightly modified. New fields were introduced into the table TRRDSITES:

ImportPos (IP), [=important positions] to compile the information on the nucleotides within transcription factor binding sites that are important for interactions with the corresponding proteins. It is filled basing on the data of methylation interference assays, transient transfection assays, and gel mobility shift assays using wild type and mutant DNA probes;
SeqContradiction (SC), [=sequence contradiction] is filled in the case when the annotator finds a discrepancy in the site sequence between the paper annotated and the corresponding data from EMBL/GenBank. The site sequence corresponding to EMBL/GenBank are indicated in the fields Sequence (SQ) of the database TRRDSITES, while the sequence from the paper annotated are given in the field SeqContradiction (SC);
PosContradiction (PC), [=positions contradiction] is filled in the case when the annotator finds a discrepancy in the site positions between the paper annotated and the corresponding data from EMBL/GenBank. The site positions corresponding to EMBL/GenBank are indicated in the fields SequencePosition (PQ) of the database TRRDSITES, while the positions from the paper annotated are given in the field PosContradiction (PC).

June 2001

TRRD Release 5.1 on-line

New section "ROS-TRRD", devoted to transcription regulation of Redox-sensitive Genes was introduced.

December 2000

New version of TRRD viewer is available

TRRD Release 5.0 on-line

1) New table TRRDUNITS was introduced. Table TRRDUNITS contains information on regulatory units (promoters, enhances, and silencers). It includes the name of regulatory unit and it's start point; localization; nucleotide sequence corresponding the regulatory unit, DNA Bank link; positions of this sequence according to the given EMBL/GenBank; left and right truncation (if the sequence is truncated); sites links; data about tissue-specificity and inducibility of regulatory unit.

2) The format was slightly modified. New fields were introduced into the table TRRDUNITS:

PromotTisSp (PT) - promoter tissue-specific characteristics:
U - ubiquitous promoter, TS - tissue-specific promoter, 0 - no data;
PromotInd (PI) - promoter induction pattern:
0 - induction from zero level, 1 - induction from basal level, 2 -induction from unknown level

December 1999

TRRD Release 4.2 on-line

The format was slightly modified. New field was introduced into the TRRDSITES table:

SiteIndex (NI) - site functionality index.

New field was introduced into the TRRDBIB table:

ArticleInd (AI) - annotation state of publications.

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