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http://www.gene-regulation.com/pub/databases.html#transcompel
Kel-Margoulis, O.1, Kel, A.1, Reuter, I.1, Deineko, I.2, Wingender, E.1
1BIOBASE GmbH, Halchtersche Strasse 33, D-38304 Wolfenbüttel, Germany
2Institute of Cytology & Genetics SB RAN, 10 Lavrentyev pr., 630090, Novosibirsk, Russia
Contact oke@biobase.de
The TRANSCompelTM database is devoted to the particular aspect of gene transcriptional regulation. It contains information about composite elements - the basic structures of combinatorial gene regulation. Composite regulatory elements consist of two closely situated binding sites for distinct transcription factors, and represent minimal functional units providing combinatorial transcriptional regulation. Both specific factor-DNA and factor-factor interactions contribute to the function of composite elements. Each database entry corresponds to an individual composite element within a particular gene and contains information about two binding sites, two corresponding transcription factors, experiments confirming cooperative action between transcription factors. interacting factors may differ by the structure of DNA-binding, activation, oligomerization and other domains. Along with structural differences, functional properties of the transcription factors and hence their specific contribution to the transcription regulation may significantly vary. Co-operative action of the transcription factors within the composite elements results in a new highly specific pattern of gene transcription that can not be provided by the involved factors separately. Composite elements are structural-functional units that provide cross-coupling of gene regulatory pathways and, in particular, cross-coupling of signal transduction pathways. There are two main types of composite elements: synergistic and antagonistic ones. In synergistic CEs, simultaneous interactions of two factors with closely situated target sites results in a non-additive high level of a transcriptional activation. Within an antagonistic CE two factors interfere with each other. Information about the structure of known composite elements and specific gene regulation achieved through such composite elements appears to be extremely useful for promoter prediction, for gene function prediction and for applied gene engineering as well. TRANSCompelTM 6.0 contains information about 256 composite regulatory elements within 162 vertebrate genes. This version of TRANSCompelTM equipped with the search and browse tools is available at http://www.gene-regulation.com/pub/databases.html#transcompel. The current professional version of the database contains description of 342 composite elements and can be obtained from BIOBASE (http://www.biobase.de). A program CATCH® for searching potential composite elements in DNA sequences has been developed. A sequence under study is scanned by this program using all composite elements collected in the TRANSCompelTM as individual searching patterns. Several parameters are available restricting the search: maximal mismatches in the cores of site1 and site2 comprising the composite elements, maximal variation of the distance between two sites, and composite score cut-off value. The composite score reflects how well the match coincides with the known examples of the composite element in the TRANSCompelTM. This scoring function takes into account the number of mismatches in both sites and the distance between them. All found matches are directly linked to the TRANSCompelTM entries containing the corresponding composite elements. Preliminary version of this program, CompelPatternSearch, is publicly available at http://compel.bionet.nsc.ru/FunSite/CompelPatternSearch.html. The current version can be obtained from BIOBASE.
Authors are grateful to Kolchanov N.A. and Romaschenko A.G. for valuable discussions on the concept of composite regulatory elements. Part of this work has been funded by Volkswagen-Stiftung (I/75941).
1. Kel-Margoulis O., Kel A.E., Reuter I., Igor V. Deineko and Wingender E. (2002) TRANSCompel - a database on composite regulatory elements in eukaryotic genes. // Nucleic Acids Res., 30, 332-334.
2. Kel-Margoulis,O.V., Romaschenko,A.G., Kolchanov,N.A., Wingender,E., and Kel,A.E. (2000) COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation. Nucleic Acids Res., 28, 311-315.
3. Heinemeyer,T., Wingender,E., Reuter,I., Hermjakob,H., Kel,A.E., Kel,O.V., Ignatieva,E.V., Ananko,E.A., Podkolodnaya,O.A., Kolpakov,F.A., Podkolodny,N.L., and Kolchanov,N.A. (1998) Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. Nucleic Acids Res., 26, 362-367.
4. Kel,O.V., Romaschenko,A.G., Kel,A.E., Wingender,E., and Kolchanov,N.A. (1997) Composite regulatory elements: classification and description in the COMPEL database. Mol. Biol. (Mosk)., 31, 498-512.
5. Wingender,E., Kel,A.E., Kel,O.V., Karas,H., Heinemeyer,T., Dietze,P., Knüppel,R., Romaschenko,A.G., and Kolchanov,N.A. (1997) TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation. Nucleic Acids Res., 25, 265-268.
6. Kel,O.V., Romaschenko,A.G., Kel,A.E., Wingender,E., and Kolchanov,N.A. (1995) A compilation of composite regulatory elements affecting gene transcription in vertebrates. Nucleic Acids Res., 23, 4097-4103.
Category Gene Identification and Structure
Go to the abstract in the NAR 2002 Database Issue.