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Bioinformatics Advance Access published online on June 5, 2007
Bioinformatics, 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

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

To whom correspondence should be addressed. Prof. Sun Kim, E-mail: sunkim2{at}indiana.edu, sebae{at}indiana.edu


  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 paper, 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

Associate Editor: Prof. Burkhard Rost

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

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