Advanced promoter analysis

State-of-the-art analysis of regulatory regions has to exceed recognition of single sites. Functional promoters, and presumably enhancers and other regulatory regions, are characterized by specific arrays of individual sites. As variable as their compositions may be, the syntax of sites in each regulatory region has to follow defined rules, which are largely unknown yet.

Therefore, the geneXplain platform provides an empirical way to identify the specific combination of sites that characterizes a given set of co-regulating promoters.

Promoter analysis for composite modules. Shown is the visualization of transcription factor binding sites (TFBSs) constituting a "promoter model", which has been computationaly generated with CMA (composite module analyst).

Complex promoter analysis, visualization of transcription factor binding sites (TFBSs) constituting a “promoter model”. (Click Image for an enlarged view.)

These specific combinations, also called “promoter models”, can be further used for screening genomic sequences or promoter databases. A comprehensive collection of mammalian promoters comes along with the TRANSFAC® database in its TRANSPRO section. The density of model matches is visualized by graded shading.

Promoter analysis for matches with a "promoter model", which comprises a set of transcription factor binding sites (TFBSs). The visualization highlights matches of those TFBSs that belong to a promoter model. The inetnsity of the background shading indicates the density of model matches.

Promoter analysis for matches with a model comprising a set of transcription factor binding sites (TFBSs). (Click Image for an enlarged view.)

×