TRANSCompel™ Documentation

TRANSCompel™ 6.0, January 2002, contains 256 composite elements.

Description: TRANSCompelTM database is originated from the COMPEL (Kel-Margoulis et. al., 2000) and collects information about composite regulatory elements (CEs) - pairs of closely situated sites and transcription factors binding to them. We define a composite element as a minimal functional unit within that both protein-DNA and protein-protein interactions contribute to a highly specific pattern of gene transcriptional regulation (Kel O.V. et al, 1995, NAR, 23: 4097-4103). The factors that cooperate at an individual CE mostly belong to different classes with respect to the structure of protein domains, namely DNA-binding and activation domain. The factors also differ in their functional properties: cell-specificity, inducibility and others. Thus, composite regulatory elements contribute to the one of the fundamental principles of genome functioning - combinatorial nature of gene transcriptional regulation.

Status: COMPEL has been developed in a joint effort of the two institutes, Institute of Cytology and Genetics in Novosibirsk, Russia, and GBF, Gesellschaft fuer Biotechnologische Forschung mbH (German Research Centre for Biotechnology GmbH) in Braunschweig, Germany. Development of COMPEL was done mainly with financial support from both the Russian and German Research Ministry, SB RAS, and from NATO until the end of 1997. In 1998, the BIOBASE GmbH granted support to update the database and to develop a relational database management system under MS Access. From this RDBMS, ASCII flat files are regularly generated. The COMPEL database has been registrated in the Federal institute of industrial ownership of the Rospatent (Moscow, Russia) as a joined property of the ICG, Russia and GBF, Braunschweig, Germany. Since Aug. 2000, BIOBASE holds distribution rights for the TRANSCompelTM and provides further update of the database as well.TRANSCompelTM database is free for non-commercial users only. For commercial users TRANSCompelTM have to be licensed. Please contact

Field description  of the TRANSCompel release 6.0.

AC Accession number of a composite element
ID Identifier of a CE
GE Gene identifier
GN Name of a gene
OS Species of a gene
SQ Sequence of a CE
ST Point relative to that positions are given
PS Positions of a CE
EM Link to EMBL
TY Type of a CE (synergism, antagonism)
CL Functional classification of the CEs (for instance, one of the factors is inducible and another is tissue-restricted)
new CM Molecular mechanism of the functioning of a CE
CC Comments to this CE
EV Accession number of evidence for this CE.
Evidence for a given CE is an experiment of certain type carried out with two individual interactions within a particular cell type.
EX Type of an experiment
CN Conclusion drawn on the base of the experiment
CT Cells (Brief name; description)
EC Comments to this evidence

IN First interaction (Accession number of an interaction; positions of the binding site).
Interaction means binding of an individual factor of a certain origin with a particular site.
FA Factor binding to this site (factor name; species; origin)
FD Factor DNA-binding domain
new FF Regulatory effect (activator or repressor)
FC Comments to this factor
TR Accession number of the factor in the TRANSFAC. This field may be repeated within the same entry.
Block starting with the field IN until the next field TR is repeated twice within the same Evidence.

RN Reference number
RA Authors
RT Title
RL Journal volume:pages (year).

// End of a composite element entry

References

1. Kel-Margoulis O., Kel A. E., Reuter I., Deineko I. V., Wingender E. (2002) "TRANSCompel® - a database on composite regulatory elements in eukaryotic genes" Nucleic Acids Res., 30, 332-334.

2. Kel-Margoulis O., Deineko I. V., Reuter I., Wingender E., Kel A. E. (2001) "TRANSCompel® - a professional database on composite regulatory elements in eukaryotic genes" Proceedings of the German Conference on Bioinformatics GCB'01. Braunschweig, Germany, October 7-10, 2001, 185-187.

3. 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.

4. Heinemeyer, T., Chen, X., Karas, H., Kel, A. E., Kel, O. V., Liebich, I., Meinhardt, T., Reuter, I., Schacherer, F., Wingender, E. (1999) "Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms." Nucleic Acids Res., 27, 318-322.

5. Kel-Margoulis, O. V., Kel, A. E., Frisch, M., Romaschenko, A. G., Kolchanov, N. A. and Wingender, E. (1998) "COMPEL - a database on composite regulatory elements." Proceedings of the First International Conference on Bioinformatics of Genome Regulation and Structure, (BGRS'98), ICG, Novosibirsk, Vol. 1, 54-57.

6. 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 transcription regulation: TRANSFAC, TRRD and COMPEL." Nucleic Acids Res., 26, 362-367.

7. Kel, O. V., Kel, A. E., Romaschenko, A. G., Wingender, E., and Kolchanov, N. A. (1997) "Composite regulatory elements: classification and description in the COMPEL database." Mol. Biol. (Mosk)., 31, 498-512.

8. 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.

9. 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.

      

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