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Nucleic Acids Research Advance Access published online on June 10, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn374
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Computational Biology

Associating transcription factor-binding site motifs with target GO terms and target genes

Mikael Bodén and Timothy L. Bailey*

Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia

*To whom correspondence should be addressed. Tel: +61 07 33462614; Fax: +61 07 33462101; Email: t.bailey{at}uq.edu.au

Received April 17, 2008. Revised May 16, 2008. Accepted May 28, 2008.

The roles and target genes of many transcription factors (TFs) are still unknown. To predict the roles of TFs, we present a computational method for associating Gene Ontology (GO) terms with TF-binding motifs. The method works by ranking all genes as potential targets of the TF, and reporting GO terms that are significantly associated with highly ranked genes. We also present an approach, whereby these predicted GO terms can be used to improve predictions of TF target genes. This uses a novel gene-scoring function that reflects the insight that genes annotated with GO terms predicted to be associated with the TF are more likely to be its targets. We construct validation sets of GO terms highly associated with known targets of various yeast and human TF. On the yeast reference sets, our prediction method identifies at least one correct GO term for 73% of the TF, 49% of the correct GO terms are predicted and almost one-third of the predicted GO terms are correct. Results on human reference sets are similarly encouraging. Validation of our target gene prediction method shows that its accuracy exceeds that of simple motif scanning.


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T. L. Bailey, M. Boden, F. A. Buske, M. Frith, C. E. Grant, L. Clementi, J. Ren, W. W. Li, and W. S. Noble
MEME SUITE: tools for motif discovery and searching
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W202 - W208.
[Abstract] [Full Text] [PDF]


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