Immunome Browser maps and visualizes queried in IEDB linear peptidic epitopes along the length of a protein sequence (a target, or reference, protein). The purpose of the tool is to allow users exploring how often each protein region has been studied in immune assays and in how many assays the immune response was positive or negative. Immunome Browser provide a summarized data by reference antigens; and the main reasons for doing that are the following: (i) epitopes reported in IEDB were identified for different strains and protein isoforms mapping to the reference – protein allows to visualize and study such epitopes as they would have the same antigen; (2) different mutant variants of the same epitope were tested and reported; and (3) immune response varies among studies and assays due to heterogeneity of samples and complexity of immune response. Immunone Browser is accessible in IEDB via two entry points (or tabs): either the Antigen or Epitope navigation paths [the latter is subject of release by 2015 and will provide functionality of changing mapping parameters and target proteins]. To get started, run the following query: and click on the Immunome Browser icon: Each selected antigen is considered to be a target protein, and the tool by default maps and visualizes all epitopes in the query result that are from the source antigen which is the target protein or any of its taxonomic child. The mapping is done using the alignment between the source antigen and the target protein and matching the epitope positions in the source antigen with the residue positions in the target protein (* -- the default mapping criteria are provided below). Note, by default, epitopes that were tested as negative for the correspondent query will be mapped as well, even if the user queried only for positive assays. Also, the epitopes that failed to satisfy the default mapping criteria won’t be mapped and visualized. Immunome Browser outputs two plots and the table. The results are query-specific! See the following figures for examples. The upper plot renders the lower (dark color) and upper (light color) bounds of the 95% confidence interval (CI) of the response frequency (RF)** for each position target protein position, averaged over all epitopes mapped to that position.
Immunome Browser maps and visualizes queried in IEDB linear peptidic epitopes along the length of a protein sequence (a target, or reference, protein). The purpose of the tool is to allow users exploring how often each protein region has been studied in immune assays and in how many assays the immune response was positive or negative. Immunome Browser provide a summarized data by reference antigens; and the main reasons for doing that are the following: (i) epitopes reported in IEDB were identified for different strains and protein isoforms – mapping to the reference protein allows to visualize and study such epitopes as they would have the same antigen; (2) different mutant variants of the same epitope were tested and reported; and (3) immune response varies among studies and assays due to heterogeneity of samples and complexity of immune response. Immunone Browser is accessible in IEDB via two entry points (or tabs): either the Antigen or Epitope navigation paths [the latter is subject of release by 2015 and will provide functionality of changing mapping parameters and target proteins]. To get started, run the following query: and click on the Immunome Browser icon: Each selected antigen is considered to be a target protein, and the tool by default maps and visualizes all epitopes in the query result that are from the source antigen which is the target protein or any of its taxonomic child. The mapping is done using the alignment between the source antigen and the target protein and matching the epitope positions in the source antigen with the residue positions in the target protein (* -- the default mapping criteria are provided below). Note, by default, epitopes that were tested as negative for the correspondent query will be mapped as well, even if the user queried only for positive assays. Also, the epitopes that failed to satisfy the default mapping criteria won’t be mapped and visualized. Immunome Browser outputs two plots and the table. The results are query-specific! See the following figures for examples. The upper plot renders the lower (dark color) and upper (light color) bounds of the 95% confidence interval (CI) of the response frequency (RF)** for each position target protein position, averaged over all epitopes mapped to that position.
ImmunomeBrowser_help.docx