Skip Navigation



Bioinformatics Advance Access published online on June 29, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl329
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
22/18/2210    most recent
btl329v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Li, L.
Right arrow Articles by Nephew, K. P.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Li, L.
Right arrow Articles by Nephew, K. P.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received April 13, 2006
Revised May 24, 2006
Accepted June 9, 2006

Article

A mixture model based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-{alpha}

Lang Li 1 *, Alfred S. L. Cheng 2, Victor X. Jin 2, Henry H. Paik 3, Meiyun Fan 3, Xiaoman Li 1, Wei Zhang 1, Jason Robarge 1, Curtis Balch 3, Ramana V. Davuluri 2, Sun Kim 3, Tim H.-M. Huang 2, and Kenneth P. Nephew 3

1 Division of Biostatistics, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 47405
2 Division of Human Cancer Genetics, Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210
3 Medical Sciences, Indiana University School of Medicine, Bloomington, IN 47405

* To whom correspondence should be addressed.
Lang Li, E-mail: lali{at}iupui.edu


  Abstract

Motivation: To detect and select patterns of transcription factor binding sites (TFBSs) which distinguish genes directly regulated by estrogen receptor-{alpha} (ER{alpha}), we developed an innovative mixture model-based discriminate analysis for identifying ordered TFBS pairs.

Results: Biologically, our proposed new algorithm clearly suggests that TFBSs are not randomly distributed within ER{alpha} target promoters (p-value < 0.001). The up-regulated targets significantly (p-value < 0.01) possess TFBS pairs, (DBP, MYC), (DBP, MYC/MAX heterodimer), (DBP, USF2), and (DBP, MYOGENIN); and down-regulated ER{alpha} target genes significantly (p-value < 0.01) possess TFBS pairs, such as (DBP, c-ETS1-68), (DBP, USF2), and (DBP, MYOGENIN). Statistically, our proposed mixture model based-discriminate analysis can simultaneously perform TFBS pattern recognition, TFBS pattern selection, and target class prediction; such integrative power cannot be achieved by current methods.

Availability: The software is available on request from the authors.

Associate Editor: Martin Bishop
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.