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  1. Restricting the input set to a few thousand regions (i.e. by picking the most robust peaks generated by a peak-calling tool) eliminates saturation of the hypergeometric test.
  2. Alternatively, results for large data sets can be viewed in the "Significant by Region-based Binomial" or "Full" View and terms enriched due to many regions clustered around one or few genes can be filtered by using the observed gene hits display filter.

This warning is not applicable when the foreground/background test test is used since the hypergeometric test is over genomic regions rather than genes.