Abstract: A method is provided for profiling regulatory factor binding sites. A complete gene is located on genome for mapping gene regulatory regions. Genomic sequences of gene regulatory regions are defined and retrieved. DNA sequence information of each retrieved gene regulatory region is screened for identifying putative regulatory factor binding sites. The putative regulatory factor binding sites are profiled.

Abstract: The invention concerns the statistical analysis of regulatory factor binding sites of differentially expressed genes. More particularly, the invention concerns methods for identifying and characterizing regulatory factor, e.g. transcription factor binding sites in differentially expressed genes in order to develop therapeutic strategies for the treatment of diseases which are accompanied by differential gene expression, or to study biological processes.