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Literature DB >> 10592253

Transcription regulatory regions database (TRRD): its status in 2000.

N A Kolchanov¹, O A Podkolodnaya, E A Ananko, E V Ignatieva, I L Stepanenko, O V Kel-Margoulis, A E Kel, T I Merkulova, T N Goryachkovskaya, T V Busygina, F A Kolpakov, N L Podkolodny, A N Naumochkin, I M Korostishevskaya, A G Romashchenko, G C Overton.

Abstract

Transcription Regulatory Regions Database (TRRD) has been developed for accumulation of experimental information on the structure-function features of regulatory regions of eukaryotic genes. Each entry in TRRD corresponds to a particular gene and contains a description of structure-function features of its regulatory regions (transcription factor binding sites, promoters, enhancers, silencers, etc.) and gene expression regulation patterns. The current release, TRRD 4.2.5, comprises the description of 760 genes, 3403 expression patterns, and >4600 regulatory elements including 3604 transcription factor binding sites, 600 promoters and 152 enhancers. This information was obtained through annotation of 2537 scientific publications. TRRD 4.2.5 is available through the WWW at http://wwwmgs.bionet.nsc.ru/mgs/dbases/trrd4/

Mesh：

Year: 2000 PMID： 10592253 PMCID： PMC102412 DOI： 10.1093/nar/28.1.298

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

8 in total

1. Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins.

Authors: M P Ponomarenko; J V Ponomarenko; A S Frolov; N L Podkolodny; L K Savinkova; N A Kolchanov; G C Overton
Journal: Bioinformatics Date: 1999 Jul-Aug Impact factor: 6.937

2. Integrated databases and computer systems for studying eukaryotic gene expression.

Authors: N A Kolchanov; M P Ponomarenko; A S Frolov; E A Ananko; F A Kolpakov; E V Ignatieva; O A Podkolodnaya; T N Goryachkovskaya; I L Stepanenko; T I Merkulova; V V Babenko; Y V Ponomarenko; A V Kochetov; N L Podkolodny; D V Vorobiev; S V Lavryushev; D A Grigorovich; Y V Kondrakhin; L Milanesi; E Wingender; V Solovyev; G C Overton
Journal: Bioinformatics Date: 1999 Jul-Aug Impact factor: 6.937

3. Transcription Regulatory Regions Database (TRRD):its status in 1999.

Authors: N A Kolchanov; E A Ananko; O A Podkolodnaya; E V Ignatieva; I L Stepanenko; O V Kel-Margoulis; A E Kel; T I Merkulova; T N Goryachkovskaya; T V Busygina; F A Kolpakov; N L Podkolodny; A N Naumochkin; A G Romashchenko
Journal: Nucleic Acids Res Date: 1999-01-01 Impact factor: 16.971

4. EpoDB: a prototype database for the analysis of genes expressed during vertebrate erythropoiesis.

Authors: C J Stoeckert; F Salas; B Brunk; G C Overton
Journal: Nucleic Acids Res Date: 1999-01-01 Impact factor: 16.971

5. Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms.

Authors: T Heinemeyer; X Chen; H Karas; A E Kel; O V Kel; I Liebich; T Meinhardt; I Reuter; F Schacherer; E Wingender
Journal: Nucleic Acids Res Date: 1999-01-01 Impact factor: 16.971

6. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999.

Authors: A Bairoch; R Apweiler
Journal: Nucleic Acids Res Date: 1999-01-01 Impact factor: 16.971

7. GeneExpress: a computer system for description, analysis, and recognition of regulatory sequences in eukaryotic genome.

Authors: N A Kolchanov; M P Ponomarenko; A E Kel; A S Frolov; F A Kolpakov; T N Goryachkovsky; O V Kel; E A Ananko; E V Ignatieva; O A Podkolodnaya; V N Babenko; I L Stepanenko; A G Romashchenko; T I Merkulova; D G Vorobiev; S V Lavryushev; A V Kochetov; G B Kolesov; V V Solovyev; L Milanesi; N L Podkolodny; E Wingender; T Heinemeyer
Journal: Proc Int Conf Intell Syst Mol Biol Date: 1998

8. GeneNet: a gene network database and its automated visualization.

Authors: F A Kolpakov; E A Ananko; G B Kolesov; N A Kolchanov
Journal: Bioinformatics Date: 1998 Impact factor: 6.937

8 in total

14 in total

1. ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another.

Authors: J V Ponomarenko; D P Furman; A S Frolov; N L Podkolodny; G V Orlova; M P Ponomarenko; N A Kolchanov; A Sarai
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

2. rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations.

Authors: J V Ponomarenko; T I Merkulova; G V Vasiliev; Z B Levashova; G V Orlova; S V Lavryushev; O N Fokin; M P Ponomarenko; A S Frolov; A Sarai
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

Transcription regulatory regions database (TRRD): its status in 2000.

1. Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins.

2. Integrated databases and computer systems for studying eukaryotic gene expression.

3. Transcription Regulatory Regions Database (TRRD):its status in 1999.

4. EpoDB: a prototype database for the analysis of genes expressed during vertebrate erythropoiesis.

5. Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms.

6. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999.

7. GeneExpress: a computer system for description, analysis, and recognition of regulatory sequences in eukaryotic genome.

8. GeneNet: a gene network database and its automated visualization.

1. ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another.

2. rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations.

3. The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data.

4. GeneNet: a database on structure and functional organisation of gene networks.

5. S/MARt DB: a database on scaffold/matrix attached regions.

6. Transcription Regulatory Regions Database (TRRD): its status in 2002.

7. Two enhancers and one silencer located in the introns of regA control somatic cell differentiation in Volvox carteri.

8. An approach to identify over-represented cis-elements in related sequences.

Review 9. Computational approaches to identify promoters and cis-regulatory elements in plant genomes.

Review 10. Network integration and graph analysis in mammalian molecular systems biology.