Performance at different overrepresentation Sig values on synthetic data. A motif was "found" if the top scoring motif returned by SCOPE overlapped the planted motif by at least 50%. Different Sig values were achieved by varying the number of upstream regions, the number of motifs per upstream region, and the number of extraneous upstream regions without planted motifs. A Sig value of 0 implies that one motif of that significance is expected by chance.
Chakravarty et al. BMC Bioinformatics 2007 8:249 doi:10.1186/1471-2105-8-249