also the identifiers that could not be mapped, if any. Since each gene in the PANTHER database belongs to a phylogenetic tree that is annotated with GO and PANTHER ontology terms and pathways, the mapped IDs from the gene list will inherit these annotations. It needs to be pointed out that, in a very rare case, a single gene symbol or its synonym can be mapped to more than one gene from the IDmapping. We are currently working with UniProt to improve such mappings. However, this is so rare that we don’t think it affects significantly to the results from the statistical tests. If the gene list is not from the 82 organisms, a user can still use the PANTHER tools, but they need to map each of their own identifiers to PANTHER identifiers first, using the downloadable PANTHER HMM scoring tool (Figure 1 and Box 2), and creating the Generic PANTHER Mapping File with two columns (the user’s ID, and the ID of the best PANTHER HMM hit) (see Box 1 for more details of the file format). Each gene in the list will inherit the same annotations as those stored in the PANTHER database for the given HMM.
