A database for metazoan immunity genes and orthologs.
These immunity genes were used as seeds to search for tentative orthologs using reciprocal protein-protein Blast searches against proteins from the GenBank and RefSeq databases. The genes, both seeds and non-seeds were clustered into 2 classes or levels of ortholog groups. These classes of ortholog group were designated according to the order of reciprocal ortholog pairs among the seed immunity genes. Briefly, in the level 1 groups, the seed genes don’t necessarily all form orthologous relationships with each other and it is possible for a non-seed gene to belong to more than one group (i.e. if it forms an orthologous pair with more than one seed gene, and the seed genes aren’t in the same ortholog group). In the level 2 groups, all the seed genes form orthologous pairs with each other and the non-seed genes are only allowed to belong to one group, the one containing the gene with whom it has the closest sequence similarity.
Our initial phylogenetic analysis suggests that this is a valid approach and attempt to collect a spectrum of immunity genes. All the immunity genes and their evidence of immune function, orthologs and ortholog groups have been combined into ImmunomeBase and it is fully searchable by:
- Species (use the binomial)
- GeneID
- Genbank Accession
- Name or keyword
- Gene Ontology ID
- Gene Ontology description
- Level 1 or 2 group ID (e.g. if known from a previous visit to the database)
