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Nucleic Acids Research, 2003, Vol. 31, No. 13 3487-3490
© 2003 Oxford University Press

REDUCE: an online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data

Crispin Roven1 and Harmen J. Bussemaker*,1,2

1 Department of Biological Sciences, Columbia University, New York, NY, USA 2 Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA

*To whom correspondence should be addressed. Tel: +1 212 854 9932; Fax: +1 212 865 8246; Email: hjb2004{at}columbia.edu

REDUCE is a motif-based regression method for microarray analysis. The only required inputs are (i) a single genome-wide set of absolute or relative mRNA abundances and (ii) the DNA sequence of the regulatory region associated with each gene that is probed. Currently supported organisms are yeast, worm and fly; it is an open question whether in its current incarnation our approach can be used for mouse or human. REDUCE uses unbiased statistics to identify oligonucleotide motifs whose occurrence in the regulatory region of a gene correlates with the level of mRNA expression. Regression analysis is used to infer the activity of the transcriptional module associated with each motif. REDUCE is available online at http://bussemaker.bio.columbia.edu/reduce/. This web site provides functionality for the upload and management of microarray data. REDUCE analysis results can be viewed and downloaded, and optionally be shared with other users or made publicly accessible.


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