Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (696K) Freely available
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 ISI Web of Science
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 arrow Search for citing articles in:
ISI Web of Science (9)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Fujibuchi, W.
Right arrow Articles by Landsman, D.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Fujibuchi, W.
Right arrow Articles by Landsman, D.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2001, Vol. 29, No. 19 3988-3996
© 2001 Oxford University Press

PROSPECT improves cis-acting regulatory element prediction by integrating expression profile data with consensus pattern searches

Wataru Fujibuchi, John S. J. Anderson and David Landsman*

Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20894, USA

Consensus pattern and matrix-based searches designed to predict cis-acting transcriptional regulatory sequences have historically been subject to large numbers of false positives. We sought to decrease false positives by incorporating expression profile data into a consensus pattern-based search method. We have systematically analyzed the expression phenotypes of over 6000 yeast genes, across 121 expression profile experiments, and correlated them with the distribution of 14 known regulatory elements over sequences upstream of the genes. Our method is based on a metric we term probabilistic element assessment (PEA), which is a ranking of potential sites based on sequence similarity in the upstream regions of genes with similar expression phenotypes. For eight of the 14 known elements that we examined, our method had a much higher selectivity than a naïve consensus pattern search. Based on our analysis, we have developed a web-based tool called PROSPECT, which allows consensus pattern-based searching of gene clusters obtained from microarray data.

* To whom correspondence should be addressed. Tel: +1 301 435 5981; Fax: +1 301 480 2918; Email: landsman{at}ncbi.nlm.nih.gov


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
Z. Barutcuoglu, R. E. Schapire, and O. G. Troyanskaya
Hierarchical multi-label prediction of gene function
Bioinformatics, April 1, 2006; 22(7): 830 - 836.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
M. Suzuki, M. G. Ketterling, and D. R. McCarty
Quantitative Statistical Analysis of cis-Regulatory Sequences in ABA/VP1- and CBF/DREB1-Regulated Genes of Arabidopsis
Plant Physiology, September 1, 2005; 139(1): 437 - 447.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
T. A. A. Harkness, K. A. Shea, C. Legrand, M. Brahmania, and G. F. Davies
A Functional Analysis Reveals Dependence on the Anaphase-Promoting Complex for Prolonged Life Span in Yeast
Genetics, October 1, 2004; 168(2): 759 - 774.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Kankainen and L. Holm
POBO, transcription factor binding site verification with bootstrapping
Nucleic Acids Res., July 1, 2004; 32(suppl_2): W222 - W229.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. E. Boardman, S. G. Oliver, and S. J. Hubbard
SiteSeer: visualisation and analysis of transcription factor binding sites in nucleotide sequences
Nucleic Acids Res., July 1, 2003; 31(13): 3572 - 3575.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H. Zhang, Y. Ramanathan, P. Soteropoulos, M. L. Recce, and P. P. Tolias
EZ-Retrieve: a web-server for batch retrieval of coordinate-specified human DNA sequences and underscoring putative transcription factor-binding sites
Nucleic Acids Res., November 1, 2002; 30(21): e121 - e121.
[Abstract] [Full Text] [PDF]


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.