| Title: | Visualization and evaluation of protein immunogens |
|---|---|
| Description: | Plots protein properties and visualizes position of peptide immunogens within protein sequence. Allows evaluation of immunogens based on structural and functional annotations to infer suitability for antibody-based methods aiming to detect native proteins. |
| Authors: | Katharina Waury [aut, cre] |
| Maintainer: | Katharina Waury <[email protected]> |
| License: | Apache License (>= 2) |
| Version: | 1.1.0 |
| Built: | 2024-10-30 08:32:57 UTC |
| Source: | https://github.com/bioc/immunogenViewer |
An immunogen is associated with a protein by adding a column to a Protein DataFrame. The immunogen is specified by a unique name. Its position is defined by either the start and end position within the protein sequence or by supplying the immunogen sequence which must be a substring of the protein's sequence.
addImmunogen(proteinDF, start = NULL, end = NULL, seq = NULL, name)addImmunogen(proteinDF, start = NULL, end = NULL, seq = NULL, name)
proteinDF |
Protein DataFrame created by call to getProteinFeatures() |
start |
Integer, start position of immunogen |
end |
Integer, end position of immunogen |
seq |
String, immunogen amino acid sequence (must be substring of protein sequence) |
name |
String, chosen name to identify immunogen |
Updated Protein DataFrame with immunogen added as a new column
proteinDF <- getProteinFeatures("P55087") proteinDF <- addImmunogen(proteinDF, start=10, end=30, name="A12") proteinDF <- addImmunogen(proteinDF, seq="RFKEAFSKAAQQTKGSYMEVEDNRSQVETDD", name="HPA")proteinDF <- getProteinFeatures("P55087") proteinDF <- addImmunogen(proteinDF, start=10, end=30, name="A12") proteinDF <- addImmunogen(proteinDF, seq="RFKEAFSKAAQQTKGSYMEVEDNRSQVETDD", name="HPA")
By calling 'evaluateImmunogen()', the immunogens associated with a Protein DataFrame can be evaluated regarding their suitability fir antibody binding in natively folded proteins. By calling the function without specifying an immunogen, all immunogens of the current protein will be evaluated. The summary DataFrame contains one row per evaluated immunogen.
evaluateImmunogen(proteinDF, immunogen = NULL)evaluateImmunogen(proteinDF, immunogen = NULL)
proteinDF |
Protein DataFrame created by call to getProteinFeatures() |
immunogen |
String, identifier name of immunogen (if not defined, all immunogens are evaluated) |
Summary DataFrame providing statistics on immunogen
proteinDF <- getProteinFeatures("P55087") proteinDF <- addImmunogen(proteinDF, start=10, end=30, name="A12") proteinDF <- addImmunogen(proteinDF, seq="RFKEAFSKAAQQTKGSYMEVEDNRSQVETDD", name="HPA") evaluateImmunogen(proteinDF, "A12") evaluateImmunogen(proteinDF)proteinDF <- getProteinFeatures("P55087") proteinDF <- addImmunogen(proteinDF, start=10, end=30, name="A12") proteinDF <- addImmunogen(proteinDF, seq="RFKEAFSKAAQQTKGSYMEVEDNRSQVETDD", name="HPA") evaluateImmunogen(proteinDF, "A12") evaluateImmunogen(proteinDF)
By providing a valid UniProt ID, information from UniProt (https://www.uniprot.org/) and PredictProtein (https://predictprotein.org/) is queried via their respective APIs. The retrieved information regarding secondary structure, solvent accessibility, membrane regions, protein-binding regions, disordered regions, PTMs and disulfide bridges is saved per residue within a Protein DataFrame. After calling 'getProteinFeatures()', immunogens can be added to the Protein DataFrame.
getProteinFeatures(uniprot, taxId = 9606)getProteinFeatures(uniprot, taxId = 9606)
uniprot |
String, UniProt ID |
taxId |
Integer, Taxonomy species ID |
Protein DataFrame
getProteinFeatures("P55087")getProteinFeatures("P55087")
'plotImmunogen()' creates multiple ggplot objects within one figure. An Immunogen DataFrame is created by filtering the Protein DataFrame for the relevant immunogen segment. A plot is created for each feature with annotations in the Immunogen DataFrame. The amino acid sequence of the immunogen is shown on the x axis.
plotImmunogen(proteinDF, immunogen)plotImmunogen(proteinDF, immunogen)
proteinDF |
Protein DataFrame created by call to getProteinFeatures() |
immunogen |
String, identifier name of immunogen |
A ggplot object
proteinDF <- getProteinFeatures("P55087") proteinDF <- addImmunogen(proteinDF, start=10, end=30, name="A12") plotImmunogen(proteinDF, "A12")proteinDF <- getProteinFeatures("P55087") proteinDF <- addImmunogen(proteinDF, start=10, end=30, name="A12") plotImmunogen(proteinDF, "A12")
A call to 'plotProtein()' visualizes all relevant protein features within one figure along the entire protein sequence. All immunogens associated with the protein are highlighted at their position along the protein sequence by darkred boxes.
plotProtein(proteinDF)plotProtein(proteinDF)
proteinDF |
Protein DataFrame created by call to getProteinFeatures() |
A ggplot object
proteinDF <- getProteinFeatures("P55087") proteinDF <- addImmunogen(proteinDF, start=10, end=30, name="A12") plotProtein(proteinDF)proteinDF <- getProteinFeatures("P55087") proteinDF <- addImmunogen(proteinDF, start=10, end=30, name="A12") plotProtein(proteinDF)
An existing immunogen is removed from a Protein DataFrame by calling 'removeImmunogen()'.
removeImmunogen(proteinDF, name)removeImmunogen(proteinDF, name)
proteinDF |
Protein DataFrame created by call to getProteinFeatures() |
name |
String, name of immunogen |
Updated Protein DataFrame with immunogen column removed
proteinDF <- getProteinFeatures("P55087") proteinDF <- addImmunogen(proteinDF, start=10, end=30, name="A12") proteinDF <- removeImmunogen(proteinDF, "A12")proteinDF <- getProteinFeatures("P55087") proteinDF <- addImmunogen(proteinDF, start=10, end=30, name="A12") proteinDF <- removeImmunogen(proteinDF, "A12")
An existing immunogen is renamed in a Protein DataFrame by calling 'renameImmunogen()'.
renameImmunogen(proteinDF, oldName, newName)renameImmunogen(proteinDF, oldName, newName)
proteinDF |
Protein DataFrame created by call to getProteinFeatures() |
oldName |
String, current name of immunogen |
newName |
String, new name of immunogen |
Updated Protein DataFrame with immunogen column renamed
proteinDF <- getProteinFeatures("P55087") proteinDF <- addImmunogen(proteinDF, start=10, end=30, name="A12") proteinDF <- renameImmunogen(proteinDF, "A12", "B12")proteinDF <- getProteinFeatures("P55087") proteinDF <- addImmunogen(proteinDF, start=10, end=30, name="A12") proteinDF <- renameImmunogen(proteinDF, "A12", "B12")