Identification of regulatory elements using a feature selection method.
BACKGROUND
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.


BACKGROUND
The software is available upon request from the first author or may be downloaded from http://www.stat.berkeley.edu/~sunduz.


BACKGROUND
keles@stat.berkeley.edu
Keleş
Sündüz
S
Division of Biostatistics, U. of California, Berkeley, CA 94720, USA. keles@stat.berkeley.edu
van der Laan
Mark
M
Eisen
Michael B
MB
D020816:Amino Acid Motifs / Q000235:genetics*; D001483:Base Sequence; D005786:Gene Expression Regulation / Q000235:genetics*; D008938:Mitosis / Q000235:genetics; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010363:Pattern Recognition, Automated; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*