Literature DB >> 9016550

TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation.

E Wingender1, A E Kel, O V Kel, H Karas, T Heinemeyer, P Dietze, R Knüppel, A G Romaschenko, N A Kolchanov.   

Abstract

Three databases that provide data on transcriptional regulation are described. TRANSFAC is a database on transcription factors and their DNA binding sites. TRRD (Transcription Regulatory Region Database) collects information about complete regulatory regions, their regulation properties and architecture. COMPEL comprises specific information on composite regulatory elements. Here, we describe the present status of these databases and the first steps towards their federation.

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Year:  1997        PMID： 9016550      PMCID： PMC146363          DOI： 10.1093/nar/25.1.265

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


  12 in total

1.  TRANSFAC retrieval program: a network model database of eukaryotic transcription regulating sequences and proteins.

Authors:  R Knüppel; P Dietze; W Lehnberg; K Frech; E Wingender
Journal:  J Comput Biol       Date:  1994       Impact factor: 1.479

Review 2.  Compilation of transcription regulating proteins.

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

3.  A compilation of composite regulatory elements affecting gene transcription in vertebrates.

Authors:  O V Kel; A G Romaschenko; A E Kel; E Wingender; N A Kolchanov
Journal:  Nucleic Acids Res       Date:  1995-10-25       Impact factor: 16.971

4.  Recognition of regulatory regions in genomic sequences.

Authors:  E Wingender
Journal:  J Biotechnol       Date:  1994-06-30       Impact factor: 3.307

Review 5.  Scaffold/matrix-attached regions: structural properties creating transcriptionally active loci.

Authors:  J Bode; T Schlake; M Ríos-Ramírez; C Mielke; M Stengert; V Kay; D Klehr-Wirth
Journal:  Int Rev Cytol       Date:  1995

6.  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

7.  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

8.  The high mobility group protein HMG I(Y) is required for NF-kappa B-dependent virus induction of the human IFN-beta gene.

Authors:  D Thanos; T Maniatis
Journal:  Cell       Date:  1992-11-27       Impact factor: 41.582

9.  Cooperativity between two NF-kappa B complexes, mediated by high-mobility-group protein I(Y), is essential for cytokine-induced expression of the E-selectin promoter.

Authors:  H Lewis; W Kaszubska; J F DeLamarter; J Whelan
Journal:  Mol Cell Biol       Date:  1994-09       Impact factor: 4.272

10.  A regulatory element that mediates co-operation between a PEA3-AP-1 element and an AP-1 site is required for phorbol ester induction of urokinase enhancer activity in HepG2 hepatoma cells.

Authors:  C Nerlov; D De Cesare; F Pergola; A Caracciolo; F Blasi; M Johnsen; P Verde
Journal:  EMBO J       Date:  1992-12       Impact factor: 11.598
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  38 in total

1.  Sequence requirements for plasmid nuclear import.

Authors:  D A Dean; B S Dean; S Muller; L C Smith
Journal:  Exp Cell Res       Date:  1999-12-15       Impact factor: 3.905

2.  COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation.

Authors:  O V Kel-Margoulis; A G Romashchenko; N A Kolchanov; E Wingender; A E Kel
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

3.  The TRANSFAC system on gene expression regulation.

Authors:  E Wingender; 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
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

4.  TRANSCompel: a database on composite regulatory elements in eukaryotic genes.

Authors:  Olga V Kel-Margoulis; Alexander E Kel; Ingmar Reuter; Igor V Deineko; Edgar Wingender
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

5.  Identification of sparsely distributed clusters of cis-regulatory elements in sets of co-expressed genes.

Authors:  Gabriel Kreiman
Journal:  Nucleic Acids Res       Date:  2004-05-20       Impact factor: 16.971

6.  MotifViz: an analysis and visualization tool for motif discovery.

Authors:  Yutao Fu; Martin C Frith; Peter M Haverty; Zhiping Weng
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

7.  Role of Runx2 in IGF-1Rβ/Akt- and AMPK/Erk-dependent growth, survival and sensitivity towards metformin in breast cancer bone metastasis.

Authors:  M Tandon; Z Chen; A H Othman; J Pratap
Journal:  Oncogene       Date:  2016-01-25       Impact factor: 9.867

8.  Definition of a T-cell receptor beta gene core enhancer of V(D)J recombination by transgenic mapping.

Authors:  R K Tripathi; N Mathieu; S Spicuglia; D Payet; C Verthuy; G Bouvier; D Depetris; M G Mattei; W M HempeL; P Ferrier
Journal:  Mol Cell Biol       Date:  2000-01       Impact factor: 4.272

9.  Human adeno-associated virus type 5 is only distantly related to other known primate helper-dependent parvoviruses.

Authors:  U Bantel-Schaal; H Delius; R Schmidt; H zur Hausen
Journal:  J Virol       Date:  1999-02       Impact factor: 5.103

10.  An array of binding sites for hepatocyte nuclear factor 4 of high and low affinities modulates the liver-specific enhancer for the human alpha1-microglobulin/bikunin precursor.

Authors:  P Rouet; G Raguenez; P Ruminy; J P Salier
Journal:  Biochem J       Date:  1998-09-15       Impact factor: 3.857
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