Skip Navigation

Nucleic Acids Research 2005 33(Web Server Issue):W432-W437; doi:10.1093/nar/gki441
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (206K) Freely available
Right arrow Screen PDF (361K) Freely available
Right arrow Supplementary Material
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Chekmenev, D. S.
Right arrow Articles by Kel, A. E.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Chekmenev, D. S.
Right arrow Articles by Kel, A. E.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

P-Match: transcription factor binding site search by combining patterns and weight matrices

D. S. Chekmenev, C. Haid and A. E. Kel*

BIOBASE GmbH Halchtersche Strasse 33, D-38304 Wolfenbüttel, Germany

*To whom correspondence should be addressed. Tel: +49 5331 8584 41; Fax: +49 5331 8584 70; Email: ake{at}biobase.de

Received February 14, 2005. Revised March 30, 2005. Accepted March 30, 2005.

P-Match is a new tool for identifying transcription factor (TF) binding sites in DNA sequences. It combines pattern matching and weight matrix approaches thus providing higher accuracy of recognition than each of the methods alone. P-Match is closely interconnected with the TRANSFAC® database. In particular, P-Match uses the matrix library as well as sets of aligned known TF-binding sites collected in TRANSFAC® and therefore provides the possibility to search for a large variety of different TF binding sites. Using results of extensive tests of recognition accuracy, we selected three sets of optimized cut-off values that minimize either false negatives or false positives, or the sum of both errors. Comparison with the weight matrix approaches such as MatchTM tool shows that P-Match generally provides superior recognition accuracy in the area of low false negative errors (high sensitivity). As familiar to the user of MatchTM, P-Match also allows to save user-specific profiles that include selected subsets of matrices with corresponding TF-binding sites or user-defined cut-off values. Furthermore, a number of tissue-specific profiles are provided that were compiled by the TRANSFAC® team. A public version of the P-Match tool is available at http://www.gene-regulation.com/cgi-bin/pub/programs/pmatch/bin/p-match.cgi.

Present address: C. Haid, Universität des Saarlandes, Saarbrücken, Germany


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Physiol. GenomicsHome page
A. Pautz, P. Rauschkolb, N. Schmidt, J. Art, M. Oelze, P. Wenzel, U. Forstermann, A. Daiber, and H. Kleinert
Effects of nitroglycerin or pentaerithrityl tetranitrate treatment on the gene expression in rat hearts: evidence for cardiotoxic and cardioprotective effects
Physiol Genomics, July 9, 2009; 38(2): 176 - 185.
[Abstract] [Full Text] [PDF]

Home page
 J. Nutr.Home page
A. Fukushima, Y. Aizaki, and K. Sakuma
Short-Chain Fatty Acids Induce Intestinal Transient Receptor Potential Vanilloid Type 6 Expression in Rats and Caco-2 Cells
J. Nutr., January 1, 2009; 139(1): 20 - 25.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
E. Wingender
The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation
Brief Bioinform, July 1, 2008; 9(4): 326 - 332.
[Abstract] [Full Text] [PDF]

Home page
 BloodHome page
L. Yu, A. J. Mohamed, O. E. Simonson, L. Vargas, K. E. M. Blomberg, B. Bjorkstrand, H. J. Arteaga, B. F. Nore, and C. I. E. Smith
Proteasome-dependent autoregulation of Bruton tyrosine kinase (Btk) promoter via NF-{kappa}B
Blood, May 1, 2008; 111(9): 4617 - 4626.
[Abstract] [Full Text] [PDF]

Home page
 CarcinogenesisHome page
B. E. Bachmeier, I. V. Mohrenz, V. Mirisola, E. Schleicher, F. Romeo, C. Hohneke, M. Jochum, A. G. Nerlich, and U. Pfeffer
Curcumin downregulates the inflammatory cytokines CXCL1 and -2 in breast cancer cells via NF{kappa}B
Carcinogenesis, April 1, 2008; 29(4): 779 - 789.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
S.-H. Tan, A. Dagvadorj, F. Shen, L. Gu, Z. Liao, J. Abdulghani, Y. Zhang, E. P. Gelmann, T. Zellweger, Z. Culig, et al.
Transcription Factor Stat5 Synergizes with Androgen Receptor in Prostate Cancer Cells
Cancer Res., January 1, 2008; 68(1): 236 - 248.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
B. Jiang, M. Q. Zhang, and X. Zhang
OSCAR: One-class SVM for accurate recognition of cis-elements
Bioinformatics, November 1, 2007; 23(21): 2823 - 2828.
[Abstract] [Full Text] [PDF]

Home page
 J. Exp. Biol.Home page
N. Jayasundara, D. W. Towle, D. Weihrauch, and C. Spanings-Pierrot
Gill-specific transcriptional regulation of Na+/K+-ATPase {alpha}-subunit in the euryhaline shore crab Pachygrapsus marmoratus: sequence variants and promoter structure
J. Exp. Biol., June 15, 2007; 210(12): 2070 - 2081.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
I. V. Deyneko, B. Bredohl, D. Wesely, Y. M. Kalybaeva, A. E. Kel, H. Blocker, and G. Kauer
FeatureScan: revealing property-dependent similarity of nucleotide sequences.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W591 - W595.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
V. Matys, O. V. Kel-Margoulis, E. Fricke, I. Liebich, S. Land, A. Barre-Dirrie, I. Reuter, D. Chekmenev, M. Krull, K. Hornischer, et al.
TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D108 - D110.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.