Identify multi-antigen signatures for improving cancer recognition by immunotherapies

This webserver was designed as a resource for developing novel immunotherapeutics that harness method-derived signatures to improve cancer recognition and limit normal tissue cross-reactions. More information can be found on the about page. Here we describe the different use cases for navigating the webserver and our associated predictions. The webserver can currently be used for three different use cases:

  1. browse based on cancer type
  2. improving upon a single antigen target
  3. evaluate antigen pairs of interest
These three use cases are laid out in more detail in the sections below.

Browse based on cancer type

The most basic starting point for navigating the Antigen Explorer webserver is to start with a cancer type of interest and view the top performing pairs.

From the main page use the dropdown menu to select your tumor type of interest and press search.
The resulting table of predictions can be sorted by clicking on the table headers.
You can also limit the values in the table to your favorite antigen or by Antigen Type by using the search bar to filter.
Once a combination of interest is found simply click the row to navigate to a page in a new window with an interactive scatterplot of expression.
All predictions are browsable at any time by selecting the browse page from the navigation bar. The same ability to sort and navigate apply.
Improving upon a single antigen target

You may already have a validated cancer antigen target, but as is often the case, this single antigen may not be specific enough. Her you can use the web server to identify secondary antigens that improve cancer discrimination, when used in combination with the primary antigen.

Starting from the main page, enter an antigen in the search box and choose a tumor type from the dropdown.
At the top of the page is a bar chart of the performance of the single antigen versus performance of the best double antigen across all predictions. A score of 1 indicates ideal discrimination. Use the table and the accompanying search feature to limit the table to a tumor type of interest. Clicking a row in the table will navigate to the specific plot view in a new tab.
Evaluate antigen pairs of interest
Finally, in a third scenario a user might start with a pair of interest and want to examine its specificity in different tumor types.
Begin by starting on the main page and entering two antigens of interest separated by a space. If the one or both members of the antigen combination are not in our database you will be presented with an error message. Sometimes an alias is to blame. Click on the associated links in the error message to verify you are using valid Entrez gene symbols.
If the genes entered are in our database, the user will be presented with an interactive scatterplot. Click and drag the mouse to select point and see a snapshot of the samples selected in the bar chart on the right hand side of the page. The donut chart on the right shows for the selected samples the number of false positives (FP) also known as the number of normal tissue samples that might cross-react in your selection. Under the donut chart precision and recall are calculated for the selected samples.
Users can switch to other tumor types via the dropdown menu in the scatterplot settings panel. Hovering over specific points in the chart will give sample identifiers for lookup at TCGA or GTEx. Clicking the gene names above the plot will navigate to HPA for more gene information.