Users can utilize the ‘Epitope Source’ panel to query CEDAR for epitopes encoded by a specific gene or protein by entering the name into the text field. As the user begins to enter text into the field, matching molecules will appear in a dynamic drop-down menu. In the example query shown in Figure 1, the antigen ‘NY-ESO-1’ was selected.
Figure 1. The Epitope Source panel
If the free-text search does not display the antigen of interest, the ‘Molecule Finder’ provides a comprehensive way to navigate the entirety of antigens cataloged in CEDAR. This tool can be accessed by clicking the Find button located next to the text field. To facilitate efficient searches through extensive sets of source antigens, the data is organized into a hierarchical tree structure. For every antigen protein in CEDAR, the corresponding organism species has been determined and mapped to specific NCBI taxonomic identifiers.
Users can explore this taxonomy tree to select an organism of interest and subsequently browse the entire set of associated genes and derived antigenic proteins. Alternatively, users may input a molecule name, UniProt identifier, or source species, to display a list of matching molecules in the bottom panel. The yellow ‘Highlight in Tree’ icon allows users to visualize a molecule’s position within the protein hierarchy, and the green ‘Apply’ icon populates the ‘Current Selection(s)’ box with the desired molecule. Multiple selections at any level of the tree can be made simultaneously when utilizing finders during a query. In the example query in Figure 2, the ‘Prostate-specific antigen’ was searched, highlighted in the tree, and selected.
Figure 2. The Molecule Finder
Additionally, users can select specific cancer-associated antigen subtypes from the ‘Epitope Source’ panel, including ‘Neoantigen’, ‘Viral antigen’, and ‘Germline/Self/Host antigen’. These three broader categories represent mutually exclusive classifications of cancer-associated antigens that can be clearly distinguished within the database.
Antigens that are not specifically cancer-associated, but were reported alongside them in a cancer-related study, can be included in a query by selecting ‘Other antigens from same reference’. The default selection on the CEDAR homepage excludes these molecules to focus on cancer-associated antigens.
Finally, for the ‘Neoantigen’ category, users can specify a specific mutation of interest at the protein level by indicating the reference amino acid, the mutation position in the source protein, and the mutated residue.