Skip Navigation



Bioinformatics Advance Access published online on April 27, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl160
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
22/14/1675    most recent
btl160v1
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 arrowRequest Permissions
Google Scholar
Right arrow Articles by Tsai, H.-K.
Right arrow Articles by Li, W.-H.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Tsai, H.-K.
Right arrow Articles by Li, W.-H.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received January 28, 2006
Revised March 24, 2006
Accepted April 21, 2006

Article

Method for identifying transcription factor binding sites in yeast

Huai-Kuang Tsai 1, Grace Tzu-Wei Huang 1, Meng-Yuan Chou 2, Henry Horng-Shing Lu 3, and Wen-Hsiung Li 4 *

1 Genomics Research Center, Academia Sinica, Taipei, 115 Taiwan
2 Institute of Information Science, Academia Sinica, Taipei, 115 Taiwan
3 Institute of Statistics, National Chiao Tung University, 1001 Ta Hsueh Road, Hsinchu 30050, Taiwan
4 Genomics Research Center, Academia Sinica, Taipei, 115 Taiwan; Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL, 60637 USA

* To whom correspondence should be addressed.
Wen-Hsiung Li, E-mail: whli{at}uchicago.edu


  Abstract

Motivation: Identifying transcription factor binding sites (TFBSs) is helpful for understanding the mechanism of transcriptional regulation. The abundance and diversity of genomic data provide an excellent opportunity for identifying TFBSs. Developing methods to integrate various types of data has become a major trend in this pursuit.

Results: We develop a TFBS identification method, TFBSfinder, which utilizes several data sources, including DNA sequences, phylogenetic information, microarray data and ChIP-chip data. For a TF, TFBSfinder rigorously selects a set of reliable target genes and a set of non-target genes (as a background set) to find over-represented and conserved motifs in target genes. A new metric for measuring the degree of conservation at a binding site across species and methods for clustering motifs and for inferring position weight matrices are proposed. For synthetic data and yeast cell cycle TFs, TFBSfinder identifies motifs that are highly similar to known consensuses. Moreover, TFBSfinder outperforms well-known methods.

Availability: http://cg1.iis.sinica.edu.tw/~TFBSfinder/.

Associate Editor: Alex Bateman
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
 BioinformaticsHome page
C.-L. Chuang, C.-H. Jen, C.-M. Chen, and G. S. Shieh
A pattern recognition approach to infer time-lagged genetic interactions
Bioinformatics, May 1, 2008; 24(9): 1183 - 1190.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
C.-Y. Chen, H.-K. Tsai, C.-M. Hsu, M.-J. May Chen, H.-G. Hung, G. T.-W. Huang, and W.-H. Li
Discovering gapped binding sites of yeast transcription factors
PNAS, February 19, 2008; 105(7): 2527 - 2532.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H.-K. Tsai, M.-Y. Chou, C.-H. Shih, G. T.-W. Huang, T.-H. Chang, and W.-H. Li
MYBS: a comprehensive web server for mining transcription factor binding sites in yeast
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W221 - W226.
[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.