EASE has an option to "enhance" the annotation for genes by including the annotation for "similar" genes. "Similar" genes are specified in a pairwise fashion in files of the \Enhance\ directory. The automated update system creates files containing "similar" LocusLink numbers as defined by four criteria:
HOMOLGENES: These genes are matched in the Homologene pair-wise flatfile.
HOMOLOGENE COGS: These genes are matched in the Homologene triplet-wise flatfile.
SAME GENE SYMBOL: These genes have the same case-insensitive gene symbol.
SAME OFFICIAL GENE SYMBOL: These genes have the same case-insensitive official gene symbol.
By checking "Enhance categorical information" or "Enhance annotation information" and clicking on the associated [select enhance methods] button, the gene information used in the over-representation analysis or annotation functions will be enhanced according to the methods selected. There are obvious caveats to doing this with respect to the danger of misleading annotation being applied to any given gene, but sometimes it is the only way to achieve acceptable levels of annotation for a given species. Since the over-representation analysis is quite robust to noisy data, the application of some spurious categorical assignments to enhance the coverage of real categorical assignments might prove beneficial.
Note that you must first update EASE with the species (most typically human) containing the "similar" genes in addition to your species of interest to take full advantage of the enhancement function.