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Literature DB >> 11125113

The TRANSFAC system on gene expression regulation.

E Wingender¹, X Chen, E Fricke, R Geffers, R Hehl, I Liebich, M Krull, V Matys, H Michael, R Ohnhäuser, M Prüss, F Schacherer, S Thiele, S Urbach.

Abstract

The TRANSFAC database on transcription factors and their DNA-binding sites and profiles (http://www.gene-regulation.de/) has been quantitatively extended and supplemented by a number of modules. These modules give information about pathologically relevant mutations in regulatory regions and transcription factor genes (PathoDB), scaffold/matrix attached regions (S/MARt DB), signal transduction (TRANSPATH) and gene expression sources (CYTOMER). Altogether, these distinct database modules constitute the TRANSFAC system. They are accompanied by a number of program routines for identifying potential transcription factor binding sites or for localizing individual components in the regulatory network of a cell.

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Year: 2001 PMID： 11125113 PMCID： PMC29801 DOI： 10.1093/nar/29.1.281

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

12 in total

1. TRANSFAC: an integrated system for gene expression regulation.

Authors: E Wingender; X Chen; R Hehl; H Karas; I Liebich; V Matys; T Meinhardt; M Prüss; I Reuter; F Schacherer
Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

2. AliBaba2: context specific identification of transcription factor binding sites.

Authors: Niels Grabe
Journal: In Silico Biol Date: 2002

3. 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

4. Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL.

Authors: T Heinemeyer; E Wingender; I Reuter; H Hermjakob; A E Kel; O V Kel; E V Ignatieva; E A Ananko; O A Podkolodnaya; F A Kolpakov; N L Podkolodny; N A Kolchanov
Journal: Nucleic Acids Res Date: 1998-01-01 Impact factor: 16.971

5. TRANSFAC database as a bridge between sequence data libraries and biological function.

Authors: E Wingender; H Karas; R Knüppel
Journal: Pac Symp Biocomput Date: 1997

Review 6. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Authors: S F Altschul; T L Madden; A A Schäffer; J Zhang; Z Zhang; W Miller; D J Lipman
Journal: Nucleic Acids Res Date: 1997-09-01 Impact factor: 16.971

Review 7. Compilation of transcription regulating proteins.

Authors: E Wingender
Journal: Nucleic Acids Res Date: 1988-03-25 Impact factor: 16.971

8. TRANSFAC: a database on transcription factors and their DNA binding sites.

Authors: E Wingender; P Dietze; H Karas; R Knüppel
Journal: Nucleic Acids Res Date: 1996-01-01 Impact factor: 16.971

9. MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data.

Authors: K Quandt; K Frech; H Karas; E Wingender; T Werner
Journal: Nucleic Acids Res Date: 1995-12-11 Impact factor: 16.971

10. IARC Database of p53 gene mutations in human tumors and cell lines: updated compilation, revised formats and new visualisation tools.

Authors: P Hainaut; T Hernandez; A Robinson; P Rodriguez-Tome; T Flores; M Hollstein; C C Harris; R Montesano
Journal: Nucleic Acids Res Date: 1998-01-01 Impact factor: 16.971

210 in total

1. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome.

Authors: Benjamin P Berman; Yutaka Nibu; Barret D Pfeiffer; Pavel Tomancak; Susan E Celniker; Michael Levine; Gerald M Rubin; Michael B Eisen
Journal: Proc Natl Acad Sci U S A Date: 2002-01-22 Impact factor: 11.205

10. EZ-Retrieve: a web-server for batch retrieval of coordinate-specified human DNA sequences and underscoring putative transcription factor-binding sites.

Authors: Haibo Zhang; Y Ramanathan; Patricia Soteropoulos; Michael L Recce; Peter P Tolias
Journal: Nucleic Acids Res Date: 2002-11-01 Impact factor: 16.971

The TRANSFAC system on gene expression regulation.

1. TRANSFAC: an integrated system for gene expression regulation.

2. AliBaba2: context specific identification of transcription factor binding sites.

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

4. Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL.

5. TRANSFAC database as a bridge between sequence data libraries and biological function.

Review 6. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Review 7. Compilation of transcription regulating proteins.

8. TRANSFAC: a database on transcription factors and their DNA binding sites.

9. MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data.

10. IARC Database of p53 gene mutations in human tumors and cell lines: updated compilation, revised formats and new visualisation tools.

1. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome.

2. The Celera Discovery System.

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

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

5. The Gene Resource Locator: gene locus maps for transcriptome analysis.

6. Nucleoprotein structure of immediate-early promoters Zp and Rp and of oriLyt of latent Epstein-Barr virus genomes.

7. rVista for comparative sequence-based discovery of functional transcription factor binding sites.

8. GALA, a database for genomic sequence alignments and annotations.

9. Additivity in protein-DNA interactions: how good an approximation is it?

10. EZ-Retrieve: a web-server for batch retrieval of coordinate-specified human DNA sequences and underscoring putative transcription factor-binding sites.