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Bioinformatics Advance Access originally published online on June 5, 2007
Bioinformatics 2007 23(19):2619-2621; doi:10.1093/bioinformatics/btm288
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

dPattern: transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis

Seung-Hee Bae 1, Haixu Tang 2, Jing Wu 4, Jun Xie 4 and Sun Kim 2,3,*

1Department of Computer Science, 2School of Informatics, 3Center for Genomics and Bioinformatics, Indiana University – Bloomington, IN 47404 and 4Department of Statistics, Purdue University, West Lafayette, IN, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Transcription factor binding sites (TFBSs) are typically short in length, thus search with a profile model from known TFBSs produces many false positives. When combined with additional information, gene expression data in this article, sensitivity and specificity of TFBS search can be improved significantly.

Results: By modifying our previous REFINEMENT approach, we developed dPattern that searches for occurrences of TFBSs in the promotor regions of up/down regulated or random genes.

Availability: http://platcom.org/projects/dpattern

Contact: sun.kim{at}acm.org or sunkim2{at}indiana.edu

Associate Editor: Burkhand Rost

Received on January 9, 2007; revised on May 20, 2007; accepted on May 21, 2007

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