Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL
T. Heinemeyer,Edgar Wingender,Ingmar Reuter,Henning Hermjakob,Alexander E. Kel,O. V. Kel,Elena V. Ignatieva,E. A. Ananko,O. A. Podkolodnaya,Fedor A. Kolpakov,N. L. Podkolodny,Nikolay A. Kolchanov +11 more
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TLDR
The quantitative and qualitative changes of all three databases and connected programs are described.Abstract:
TRANSFAC, TRRD (Transcription Regulatory Region Database) and COMPEL are databases which store information about transcriptional regulation in eukaryotic cells. The three databases provide distinct views on the components involved in transcription: transcription factors and their binding sites and binding profiles (TRANSFAC), the regulatory hierarchy of whole genes (TRRD), and the structural and functional properties of composite elements (COMPEL). The quantitative and qualitative changes of all three databases and connected programs are described. The databases are accessible via WWW:http://transfac.gbf.de/TRANSFAC orhttp://www.bionet.nsc.ru/TRRDread more
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Plant cis-acting regulatory DNA elements (PLACE) database: 1999
TL;DR: This report summarizes the present status of this database of nucleotide sequence motifs found in plant cis-acting regulatory DNA elements and available tools.
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TRANSFAC®: transcriptional regulation, from patterns to profiles
V. Matys,Ellen Fricke,Robert Geffers,Ellen Gößling,Martin Haubrock,Reinhard Hehl,Klaus Hornischer,Dagmar Karas,Alexander E. Kel,Olga V. Kel-Margoulis,Dorothee-U. Kloos,Sigrid Land,Birgit Lewicki-Potapov,Holger Michael,Richard Münch,Ingmar Reuter,Stella Rotert,H. Saxel,Maurice Scheer,S. Thiele,Edgar Wingender +20 more
TL;DR: The TRANSFAC database on eukaryotic transcriptional regulation, comprising data on transcription factors, their target genes and regulatory binding sites, has been extended and further developed, both in number of entries and in the scope and structure of the collected data.
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References
More filters
Journal ArticleDOI
MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data.
TL;DR: A set of tools for molecular biologists that allow generation of new matrix and detection of potential sequence matches by automatic searches with a library of pre-compiled matrices is presented in this article.
Journal ArticleDOI
TRANSFAC: a database on transcription factors and their DNA binding sites.
TL;DR: This report summarizes the present status of this database and accompanying retrieval tools about eukaryotic transcription regulating DNA sequence elements and the transcription factors binding to and acting through them.
Journal ArticleDOI
Selection of DNA Binding Sites by Regulatory Proteins Statistical-mechanical Theory and Application to Operators and Promoters
Otto G. Berg,Peter H. von Hippel +1 more
TL;DR: A statistical-mechanical selection theory for the sequence analysis of a set of specific DNA regulatory sites makes it possible to predict the relationship between individual base-pair choices in the site and specific activity (affinity), and shows that functional specificity is based on other properties in addition to primary sequence recognition.
Book ChapterDOI
SRS: information retrieval system for molecular biology data banks.
TL;DR: SRS is an integrated system that provides a homogeneous interface to all flat file data banks retained in their original format, a retrieval system that allows access to, but not the depositing of, data.
Journal ArticleDOI
Compilation and analysis of eukaryotic POL II promoter sequences.
TL;DR: Application of this technique to E. coli promoters as a control ensemble revealed the well known consensus sequences at -35 and -10 which indicates that the methods are adequate to approach problems of this kind.