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Bioinformatics Advance Access published online on April 27, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl160
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© 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
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