ImmunomeBrowser: a tool to aggregate and visualize complex and heterogeneous epitopes in reference proteins

被引：33

作者：

Dhanda, Sandeep Kumar ^{[1
]}

Vita, Randi ^{[1
]}

Ha, Brendan ^{[1
]}

Grifoni, Alba ^{[1
]}

Peters, Bjoern ^{[1
,2
]}

Sette, Alessandro ^{[1
,2
]}

机构：

[1] La Jolla Inst Allergy & Immunol, Div Vaccine Discovery, La Jolla, CA 92037 USA

[2] Univ Calif San Diego, Dept Med, La Jolla, CA 92093 USA

来源：

BIOINFORMATICS | 2018年 / 34卷 / 22期

关键词：

IMMUNOGENICITY;

D O I：

10.1093/bioinformatics/bty463

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: Datasets that are derived from different studies (e.g. MHC ligand elution, MHC binding, B/T cell epitope screening etc.) often vary in terms of experimental approaches, sizes of peptides tested, including partial and or nested overlapping peptides and in the number of donors tested. Results: We present a customized application of the Immune Epitope Database's ImmunomeBrowser tool, which can be used to effectively aggregate and visualize heterogeneous immunological data. User provided peptide sets and associated response data is mapped to a user-provided protein reference sequence. The output consists of tables and figures representing the aggregated data represented by a Response Frequency score and associated estimated confidence interval. This allows the user to visualizing regions associated with dominant responses and their boundaries. The results are presented both as a user interactive javascript based web interface and a tabular format in a selected reference sequence.

引用

页码：3931 / 3933

页数：3

共 11 条

[1] Computational Tools for the Identification and Interpretation of Sequence Motifs in Immunopeptidomes [J].

Alvarez, Bruno ;

Barra, Carolina ;

Nielsen, Morten ;

Andreatta, Massimo .

PROTEOMICS, 2018, 18 (12)

[2] Rational design of stable and functional hirudin III mutants with lower antigenicity [J].

Asgari, Saeme ;

Mirzahoseini, Hasan ;

Karimipour, Morteza ;

Rahimi, Hamze ;

Ebrahim-Habibi, Azadeh .

BIOLOGICALS, 2015, 43 (06) :479-491

[3] Development of a strategy and computational application to select candidate protein analogues with reduced HLA binding and immunogenicity [J].

Dhanda, Sandeep Kumar ;

Grifoni, Alba ;

Pham, John ;

Vaughan, Kerrie ;

Sidney, John ;

Peters, Bjoern ;

Sette, Alessandro .

IMMUNOLOGY, 2018, 153 (01) :118-132

[4] T-cell dependent immunogenicity of protein therapeutics: Preclinical assessment and mitigation [J].

Jawa, Vibha ;

Cousens, Leslie P. ;

Awwad, Michel ;

Wakshull, Eric ;

Kropshofer, Harald ;

De Groot, Anne S. .

CLINICAL IMMUNOLOGY, 2013, 149 (03) :534-555

[5] A Meta-Analysis of the Existing Knowledge of Immunoreactivity against Hepatitis C Virus (HCV) [J].

Kim, Yohan ;

Vaughan, Kerrie ;

Greenbaum, Jason ;

Peters, Bjoern ;

Law, Mansun ;

Sette, Alessandro .

PLOS ONE, 2012, 7 (05)

[6]

Li Pira G., 2010, J BIOMED BIOTECHNOL, V2010, DOI DOI 10.1155/2010/325720

[7] Computationally optimized deimmunization libraries yield highly mutated enzymes with low immunogenicity and enhanced activity [J].

Salvat, Regina S. ;

Verma, Deeptak ;

Parker, Andrew S. ;

Kirsch, Jack R. ;

Brooks, Seth A. ;

Bailey-Kellogg, Chris ;

Griswold, Karl E. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2017, 114 (26) :E5085-E5093

[8] Comprehensive Analysis of the Naturally Processed Peptide Repertoire: Differences between HLA-A and B in the Immunopeptidome [J].

Schellens, Ingrid M. M. ;

Hoof, Ilka ;

Meiring, Hugo D. ;

Spijkers, Sanne N. M. ;

Poelen, Martien C. M. ;

van Gaans-van den Brink, Jacqueline A. M. ;

van der Poel, Kees ;

Costa, Ana I. ;

van Els, Cecile A. C. M. ;

van Baarle, Debbie ;

Kesmir, Can .

PLOS ONE, 2015, 10 (09)

[9] Producing nature's gene-chips: The generation of peptides for display by MHC class I molecules [J].

Shastri, N ;

Schwab, S ;

Serwold, T .

ANNUAL REVIEW OF IMMUNOLOGY, 2002, 20 :463-493

[10] Deciphering the MHC-associated peptidome: a review of naturally processed ligand data [J].

Vaughan, Kerrie ;

Xu, Xiaojun ;

Caron, Etienne ;

Peters, Bjoern ;

Sette, Alessandro .

EXPERT REVIEW OF PROTEOMICS, 2017, 14 (09) :729-736

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