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REDUCE
REDUCE is an acronym that stands for Regulatory Element Detection Using Correlation with Expression, not coincidentally also the title of our paper. Based on a simple model for transcriptional regulation by independently acting transcription factors, REDUCE makes it possible to find regulatory elements based on a single microarray experiment. There is no need to first cluster genes on the basis of their expression profiles over multiple experiments, and there are no parameters to be tuned. Although the underlying model for transcriptional activation represents a gross simplification of the molecular details, our work can be seen as a first attempt to "reduce" the complexity of the genome-wide expression pattern by understanding it in terms of a relatively small number of parameters, representing the combined transcription factor activities or "regulome".
A sample input file for Saccharomyces
cerevisiae can be downloaded here.
Another sample file for
Candida albicans is also available. This dataset is based on the work of
Lorenz et al., corresponding to the wild-type strain SC5314
exposed to macrophages for one hour. The expression ratio was log2
transformed. Please note that the server currently takes only
ORF19 names because ORF6 contains many mistakes which have
been corrected in version 19. The upstream sequence used in this server was
downloaded from Biotechnology Research
Institute (National Research Council, Canada).
Please direct all questions to the administrator.
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