Detecting Transcriptional cis-Regulation from Gene Expression Data
The regulation of gene expression in eukaryotes is a complex process still to be elucidated. It has been known for a long time that the coordinated actions of particular transcription factors play a fundamental role in this process, but discovering such cis-regulatory actions remains a challenging problem, both experimentally and computationally. We have developed a systematic approach to discover combinations of regulatory motifs which potentially regulate certain genes under certain conditions, using gene expression data obtained from microarray experiments. Given a list of motifs and a table of microarray data, our method returns a ranked list of motif combinations which seem to play a particular role in the regulation of gene expression. We applied this method to track cis-regulatory factors in the yeast S. cerevisiae, using a compilation of public microarray data in combination with a list of known or putative transcription factor binding site motifs.