Automatic extraction of position specific cooccurrence of transcription factor bindings on promoters

The difficulty 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 specific if we assume chemical interaction. Such traces can thus be stochastically extracted by aligning many promoters. Our new method, named POSTSCRIPTER, automatically identifies position specificity of each factor binding site, and also calculates their cooccurrency for significance measuring. Applying these to 237 promoters, we extracted novel coincident patterns. They suggest unseen interaction which we will discuss.