It is worth pointing out that there are other similar tools to perform overrepresentation and enrichment tests, most notably, GSEA32 and DAVID33. Although all three tools use very similar statistical algorithms in the back end, there are some differences among them. GSEA requires download and installation, so its targeted users are bioinformaticians who are more computer-savvy. Both DAVID and PANTHER are online tools and are more appealing to bench biologists. Compared to DAVID, PANTHER has a few advantages. First, PANTHER is currently part of the GO consortium, and integrates more updated GO curation data with the tools. In fact, DAVID downloads PANTHER data and integrate them in its analysis tools. Second, PANTHER allows users to analyze genome data from 82 organisms using the online tool, and any other organisms using the PANTHER scoring tool. Third, the phylogenetic trees in PANTHER protein library allow users to make more accurate ortholog prediction, and thus greatly enhance the capability of the tools. One weakness of PANTHER is that it cannot analyze data against resources outside of PANTHER, such as KEGG and Reactome.
