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Nucleic Acids Research 2004 32(21):6212-6217; doi:10.1093/nar/gkh943
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Published online 1 December 2004

Nucleic Acids Research, Vol. 32 No. 21 © Oxford University Press 2004; all rights reserved

Computational method for discovery of estrogen responsive genes

Suisheng Tang, Sin Lam Tan, Suresh Kumar Ramadoss, Arun Prashanth Kumar, Man-Hung Eric Tang and Vladimir B. Bajic*

Knowledge Extraction Lab, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613

* To whom correspondence should be addressed. Tel: +65 6874 8800; Fax: +65 6774 8056; E-mail: bajicv{at}i2r.a-star.edu.sg

Received July 2, 2004; Revised September 8, 2004; Accepted October 28, 2004

Estrogen has a profound impact on human physiology and affects numerous genes. The classical estrogen reaction is mediated by its receptors (ERs), which bind to the estrogen response elements (EREs) in target gene's promoter region. Due to tedious and expensive experiments, a limited number of human genes are functionally well characterized. It is still unclear how many and which human genes respond to estrogen treatment. We propose a simple, economic, yet effective computational method to predict a subclass of estrogen responsive genes. Our method relies on the similarity of ERE frames across different promoters in the human genome. Matching ERE frames of a test set of 60 known estrogen responsive genes to the collection of over 18 000 human promoters, we obtained 604 candidate genes. Evaluating our result by comparison with the published microarray data and literature, we found that more than half (53.6%, 324/604) of predicted candidate genes are responsive to estrogen. We believe this method can significantly reduce the number of testing potential estrogen target genes and provide functional clues for annotating part of genes that lack functional information.


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