Automatic Extraction of Position Speci c Cooccurrence of Transcription Factor Bindings on Promoters

The di culty of analyzing eukaryotic Pol II promoters originates in complex interaction between various transcription factors. Every precise investigation requires much labor. It is time consuming. However, promoters themselves conserve signs of such interaction. Each binding site will be position speci c if we assume chemical interaction. Such traces can thus be stochastically extracted by aligning many promoters. Our new method, named POSTSCRIPTER, automatically identi es position speci city of each factor binding site, and also calculates their cooccurency for signi cance measuring. Applying these to 237 promoters, we extracted novel coincident patterns. They suggest unseen interaction, which we will discuss.