Bioinformatics Vol. 18 no. 9 2002
Pages 1167-1175
© 2002 Oxford University Press
Identification of regulatory elements using a feature selection method
1,*
1 Division of Biostatistics, U. of California,
Berkeley, CA 94720, USA
2 Department of Molecular and Cell Biology,
University of California, Berkeley, CA 94720, USA
3 Life Sciences Division, Ernest Orlando Lawrence Berkeley National Lab,
Berkeley, CA 94720, USA
Received on January 19, 2002
; revised on February 20, 2002
; accepted on March 21, 2002
Motivation: Many methods have been described to identify regulatory motifs in the transcription control regions of genes that exhibit similar patterns of gene expression across a variety of experimental conditions. Here we focus on a single experimental condition, and utilize gene expression data to identify sequence motifs associated with genes that are activated under this experimental condition. We use a linear model with two-way interactions to model gene expression as a function of sequence features (words) present in presumptive transcription control regions. The most relevant features are selected by a feature selection method called stepwise selection with monte carlo cross validation. We apply this method to a publicly available dataset of the yeast Saccharomyces cerevisiae, focussing on the 800 basepairs immediately upstream of each gene's translation start site (the upstream control region (UCR)).
Results: We successfully identify regulatory motifs that are known to be active under the experimental conditions analyzed, and find additional significant sequences that may represent novel regulatory motifs. We also discuss a complementary method that utilizes gene expression data from a single microarray experiment and allows averaging over variety of experimental conditions as an alternative to motif finding methods that act on clusters of co-expressed genes.
Availability: The software is available upon request from the first author or may be downloaded from http://www.stat.berkeley.edu/~sunduz.
Contact: keles{at}stat.berkeley.edu
* To whom correspondence should be addressed.
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