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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Selected References
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- Bode J., Schlake T., Ríos-Ramírez M., Mielke C., Stengert M., Kay V., Klehr-Wirth D. Scaffold/matrix-attached regions: structural properties creating transcriptionally active loci. Int Rev Cytol. 1995;162A:389–454. doi: 10.1016/s0074-7696(08)61235-8. [DOI] [PubMed] [Google Scholar]
- Bucher P., Trifonov E. N. Compilation and analysis of eukaryotic POL II promoter sequences. Nucleic Acids Res. 1986 Dec 22;14(24):10009–10026. doi: 10.1093/nar/14.24.10009. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kel O. V., Romaschenko A. G., Kel A. E., Wingender E., Kolchanov N. A. A compilation of composite regulatory elements affecting gene transcription in vertebrates. Nucleic Acids Res. 1995 Oct 25;23(20):4097–4103. doi: 10.1093/nar/23.20.4097. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Knüppel R., Dietze P., Lehnberg W., Frech K., Wingender E. TRANSFAC retrieval program: a network model database of eukaryotic transcription regulating sequences and proteins. J Comput Biol. 1994 Fall;1(3):191–198. doi: 10.1089/cmb.1994.1.191. [DOI] [PubMed] [Google Scholar]
- Lewis H., Kaszubska W., DeLamarter J. F., Whelan J. 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. Mol Cell Biol. 1994 Sep;14(9):5701–5709. doi: 10.1128/mcb.14.9.5701. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Nerlov C., De Cesare D., Pergola F., Caracciolo A., Blasi F., Johnsen M., Verde P. 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. EMBO J. 1992 Dec;11(12):4573–4582. doi: 10.1002/j.1460-2075.1992.tb05559.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Quandt K., Frech K., Karas H., Wingender E., Werner T. MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res. 1995 Dec 11;23(23):4878–4884. doi: 10.1093/nar/23.23.4878. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Thanos D., Maniatis T. The high mobility group protein HMG I(Y) is required for NF-kappa B-dependent virus induction of the human IFN-beta gene. Cell. 1992 Nov 27;71(5):777–789. doi: 10.1016/0092-8674(92)90554-p. [DOI] [PubMed] [Google Scholar]
- Wingender E. Compilation of transcription regulating proteins. Nucleic Acids Res. 1988 Mar 25;16(5):1879–1902. doi: 10.1093/nar/16.5.1879. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wingender E., Dietze P., Karas H., Knüppel R. TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Res. 1996 Jan 1;24(1):238–241. doi: 10.1093/nar/24.1.238. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wingender E. Recognition of regulatory regions in genomic sequences. J Biotechnol. 1994 Jun 30;35(2-3):273–280. doi: 10.1016/0168-1656(94)90041-8. [DOI] [PubMed] [Google Scholar]
- Wood L. D., Farmer A. A., Richmond A. HMGI(Y) and Sp1 in addition to NF-kappa B regulate transcription of the MGSA/GRO alpha gene. Nucleic Acids Res. 1995 Oct 25;23(20):4210–4219. doi: 10.1093/nar/23.20.4210. [DOI] [PMC free article] [PubMed] [Google Scholar]