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Bioinformatics Advance Access originally published online on November 30, 2006
Bioinformatics 2007 23(4):493-495; doi:10.1093/bioinformatics/btl607
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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.


  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 (PLSs) based regression 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.

Contact: pl219{at}cam.ac.uk

Associate Editor: Martin Bishop

Received on September 19, 2006; revised on November 23, 2006; accepted on November 23, 2006

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