T-Reg Comparator: an analysis tool for the comparison of position weight matrices

Röpcke S, Grossmann S, Rahmann S, Vingron M (2005)
Nucleic Acids Research 33(Web Server): W438-W441.

Download
OA
Journal Article | Published | English
Author
; ; ;
Abstract
T-Reg Comparator is a novel software tool designed to support research into transcriptional regulation. Sequence motifs representing transcription factor binding sites are usually encoded as position weight matrices. The user inputs a set of such weight matrices or binding site sequences and our program matches them against the T-Reg database, which is presently built on data from the Transfac [E. Wingender (2004) In Silico Biol., 4, 55-61] and Jaspar [A. Sandelin, W. Alkema, P. Engstrom, W. W. Wasserman and B. Lenhard (2004) Nucleic Acids Res., 32, D91-D94]. Our tool delivers a detailed report on similarities between user-supplied motifs and motifs in the database. Apart from simple one-to-one relationships, T-Reg Comparator is also able to detect similarities between submatrices. In addition, we provide a user interface to a program for sequence scanning with weight matrices. Typical areas of application for T-Reg Comparator are motif and regulatory module finding and annotation of regulatory genomic regions. T-Reg Comparator is available at http://treg.molgen.mpg.de.
Publishing Year
ISSN
eISSN
PUB-ID

Cite this

Röpcke S, Grossmann S, Rahmann S, Vingron M. T-Reg Comparator: an analysis tool for the comparison of position weight matrices. Nucleic Acids Research. 2005;33(Web Server):W438-W441.
Röpcke, S., Grossmann, S., Rahmann, S., & Vingron, M. (2005). T-Reg Comparator: an analysis tool for the comparison of position weight matrices. Nucleic Acids Research, 33(Web Server), W438-W441.
Röpcke, S., Grossmann, S., Rahmann, S., and Vingron, M. (2005). T-Reg Comparator: an analysis tool for the comparison of position weight matrices. Nucleic Acids Research 33, W438-W441.
Röpcke, S., et al., 2005. T-Reg Comparator: an analysis tool for the comparison of position weight matrices. Nucleic Acids Research, 33(Web Server), p W438-W441.
S. Röpcke, et al., “T-Reg Comparator: an analysis tool for the comparison of position weight matrices”, Nucleic Acids Research, vol. 33, 2005, pp. W438-W441.
Röpcke, S., Grossmann, S., Rahmann, S., Vingron, M.: T-Reg Comparator: an analysis tool for the comparison of position weight matrices. Nucleic Acids Research. 33, W438-W441 (2005).
Röpcke, Stefan, Grossmann, Steffen, Rahmann, Sven, and Vingron, Martin. “T-Reg Comparator: an analysis tool for the comparison of position weight matrices”. Nucleic Acids Research 33.Web Server (2005): W438-W441.
Main File(s)
File Name
Access Level
OA Open Access

This data publication is cited in the following publications:
This publication cites the following data publications:

27 Citations in Europe PMC

Data provided by Europe PubMed Central.

A discriminative approach for unsupervised clustering of DNA sequence motifs.
Stegmaier P, Kel A, Wingender E, Borlak J., PLoS Comput. Biol. 9(3), 2013
PMID: 23555204

17 References

Data provided by Europe PubMed Central.

JASPAR: an open-access database for eukaryotic transcription factor binding profiles.
Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B., Nucleic Acids Res. 32(Database issue), 2004
PMID: 14681366
Fitting a mixture model by expectation maximization to discover motifs in biopolymers.
Bailey TL, Elkan C., Proc Int Conf Intell Syst Mol Biol 2(), 1994
PMID: 7584402
A SELEX primer.
Fitzwater T, Polisky B., Meth. Enzymol. 267(), 1996
PMID: 8743323
Similarity of position frequency matrices for transcription factor binding sites.
Schones DE, Sumazin P, Zhang MQ., Bioinformatics 21(3), 2005
PMID: 15319260
A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes.
Thijs G, Marchal K, Lescot M, Rombauts S, De Moor B, Rouze P, Moreau Y., J. Comput. Biol. 9(2), 2002
PMID: 12015892
Computational detection of cis -regulatory modules.
Aerts S, Van Loo P, Thijs G, Moreau Y, De Moor B., Bioinformatics 19 Suppl 2(), 2003
PMID: 14534164
On the power of profiles for transcription factor binding site detection
Rahmann S., Müller T., Vingron M.., 2003
TESS: Transcription Element Search Software on the WWW Technical Report CBIL-TR-1997-1001-v0.0
Schug J., Overton G.C.., 1997
In vitro selection of specific RNA inhibitors of NFATc.
Bae SJ, Oum JH, Sharma S, Park J, Lee SW., Biochem. Biophys. Res. Commun. 298(4), 2002
PMID: 12408978

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 15980506
PubMed | Europe PMC

Search this title in

Google Scholar