Skip Navigation



Bioinformatics Advance Access published online on November 30, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl607
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
23/4/493    most recent
btl607v1
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 Brilli, M.
Right arrow Articles by Lió, P.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Brilli, M.
Right arrow Articles by Lió, 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 September 19, 2006
Revised November 23, 2006
Accepted November 23, 2006

Applications note

MotifScorer: using a compendium of microarrays to identify regulatory motifs

Matteo Brilli 1, Renato Fani 1, and Pietro Lió 2 *

1 Dipartimento di Biologia Animale e Genetica, via Romana 17, 50125 Firenze, Italy
2 Computer Laboratory, University of Cambridge, Cambridge CB3 0FD, UK

* To whom correspondence should be addressed.
Pietro Lió, E-mail: pl219{at}cam.ac.uk


  Abstract

Summary: We describe MotifScorer, a program for systematic genome-wide identification of transcription sites. The program uses a compendium of gene expression microarrays and implements state-of-art partial least squares based regression (PLS) and stepwise regression procedures. Candidate motifs from the upstream sequences of groups of co-regulated genes are identified and assigned a score using genomic background models and available motif finding tools. The use of a large library of expression data allows statistical comparative analysis of the specificity of motifs identified in different conditions.

Availability: MotifScorer, which is written in Java and Matlab, manual and example files are available 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?


This article has been cited by other articles:


Home page
 Brief BioinformHome page
M. Brilli, R. Fani, and P. Lio
Current trends in the bioinformatic sequence analysis of metabolic pathways in prokaryotes
Brief Bioinform, January 1, 2008; 9(1): 34 - 45.
[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.