Bioinformatics Advance Access originally published online on April 27, 2006
Bioinformatics 2006 22(14):1675-1681; doi:10.1093/bioinformatics/btl160
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method for identifying transcription factor binding sites in yeast
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 Department of Ecology and Evolution, University of Chicago 1101 East 57th Street, Chicago, IL 60637, USA
*To whom correspondence should be addressed.
Motivation: Identifying transcription factor binding sites (TFBSs) is helpful for understanding the mechanism of transcriptional regulation. The abundance and the 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 overrepresented 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/
Contact: whli{at}uchicago.edu
Supplementary information: Supplementary data are available on Bioinformatics online.
Received on January 28, 2006; revised on March 24, 2006; accepted on April 21, 2006
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  K. B. S. Swamy, C.-Y. Cho, S. Chiang, Z. T.-Y. Tsai, and H.-K. Tsai Impact of DNA-binding position variants on yeast gene expression Nucleic Acids Res., September 18, 2009; (2009) gkp743v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y.-M. Chang, H.-F. Juan, T.-Y. Lee, Y.-Y. Chang, Y.-M. Yeh, W.-H. Li, and A. C.-C. Shih Prediction of human miRNAs using tissue-selective motifs in 3' UTRs PNAS, November 4, 2008; 105(44): 17061 - 17066. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|