EASE also includes these advanced features:

- True multiplicity-adjusted p-values for categories using a bootstrap method. This is important for determining the "real" p-value of a given category given the sheer number of statistical tests performed.

- Enhancement of gene annotation and categorical information by applying the annotation of orthologous genes. This option is important for enabling over-representation analysis in poorly annotated species, and for filling in the gaps of knowledge of the genes in such species by including knowledge from the same genes in other species.

- Turning turn gene lists themselves into "gene categories" for use in EASE analyses of future experiments. This allows researchers to quickly ascertain significant overlaps with the clusters in any number of previous experiments.

- Over-representation in all pair-wise gene categories. This feature allows a fine-tuned theme detection that might be missed by looking only at over-representation in individual categories.

- Limiting the genes analyzed to a particular set of categories. This enables answers to questions like "What is special about the cell-signaling genes in my results compared to all cell-signaling genes represented on my microarray?"

- Compare gene lists at a thematic level. The comparative analysis feature of EASE allows the researcher to determine the biological themes that most differentiate two gene lists.