The binding of transcription factors to specific regulatory sequence elements is 
a primary mechanism for controlling gene transcription. Eukaryotic genes are 
often regulated by several transcription factors whose binding sites are tightly 
clustered and form cis-regulatory modules. In this paper, we present a web 
server, CREME, for identifying and visualizing cis-regulatory modules in the 
promoter regions of a given set of potentially co-regulated genes. CREME relies 
on a database of putative transcription factor binding sites that have been 
annotated across the human genome using a library of position weight matrices 
and evolutionary conservation with the mouse and rat genomes. A search algorithm 
is applied to this data set to identify combinations of transcription factors 
whose binding sites tend to co-occur in close proximity in the promoter regions 
of the input gene set. The identified cis-regulatory modules are statistically 
scored and significant combinations are reported and graphically visualized. Our 
web server is available at http://creme.dcode.org.