MCVdb: A database for knowledge discovery in Merkel cell polyomavirus with applications in T cell immunology and vaccinology

Guang Lan Zhang; James A. DeCaprio; Lou Chitkushev; Derin B. Keskin; Catherine J. Wu; Vladimir Brusic

doi:10.1109/BIBM.2017.8217881

MCVdb: A database for knowledge discovery in Merkel cell polyomavirus with applications in T cell immunology and vaccinology

Guang Lan Zhang, James A. DeCaprio, Lou Chitkushev, Derin B. Keskin, Catherine J. Wu, Vladimir Brusic

Research output: Chapter in Book/Conference proceeding › Conference contribution › peer-review

1 Citation (Scopus)

Abstract

Merkel Cell Polyomavirus (MCV) is associated with more than 80% of Merkel cell carcinoma (MCC), a rare but highly lethal form of skin cancer. We made use of the immunological data on MCV available through publications and databases and constructed MCV T cell Antigen Database (MCVdb). MCVdb contains 734 curated antigen entries of MCV antigenic proteins and 30 experimentally verified T cell epitopes. The data were subject to extensive quality control (redundancy elimination, error detection, and vocabulary consolidation). A set of computational tools for in-depth analysis, such as sequence comparison using BLAST search, multiple alignments of antigens, and T cell epitope conservation analysis have been integrated within the MCVdb. Predicted Class I and Class II HLA-binding peptides for 15 common HLA alleles are included in this database as putative targets. MCVdb is a unique data source providing a comprehensive list of MCV antigens and peptides. MCVdb is publicly available at http://projects.met-hilab.org/mcv/.

Original language	English
Title of host publication	Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Editors	Illhoi Yoo, Jane Huiru Zheng, Yang Gong, Xiaohua Tony Hu, Chi-Ren Shyu, Yana Bromberg, Jean Gao, Dmitry Korkin
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	1483-1488
Number of pages	6
ISBN (Electronic)	9781509030491
DOIs	https://doi.org/10.1109/BIBM.2017.8217881
Publication status	Published - 15 Dec 2017
Externally published	Yes
Event	2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 - Kansas City, United States Duration: 13 Nov 2017 → 16 Nov 2017

Publication series

Name	Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Volume	2017-January

Conference

Conference	2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Country/Territory	United States
City	Kansas City
Period	13/11/17 → 16/11/17

Keywords

Cancer vaccine
Merkel cell carcinoma
Merkel cell polyomavirus
T cell epitope

ASJC Scopus subject areas

Biomedical Engineering
Health Informatics

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1109/BIBM.2017.8217881

Cite this

Zhang, G. L., DeCaprio, J. A., Chitkushev, L., Keskin, D. B., Wu, C. J., & Brusic, V. (2017). MCVdb: A database for knowledge discovery in Merkel cell polyomavirus with applications in T cell immunology and vaccinology. In I. Yoo, J. H. Zheng, Y. Gong, X. T. Hu, C.-R. Shyu, Y. Bromberg, J. Gao, & D. Korkin (Eds.), Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 (pp. 1483-1488). (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; Vol. 2017-January). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2017.8217881

Zhang, Guang Lan ; DeCaprio, James A. ; Chitkushev, Lou et al. / MCVdb : A database for knowledge discovery in Merkel cell polyomavirus with applications in T cell immunology and vaccinology. Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. editor / Illhoi Yoo ; Jane Huiru Zheng ; Yang Gong ; Xiaohua Tony Hu ; Chi-Ren Shyu ; Yana Bromberg ; Jean Gao ; Dmitry Korkin. Institute of Electrical and Electronics Engineers Inc., 2017. pp. 1483-1488 (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017).

@inproceedings{37f4b36c1eb64ad1b32ce64104897230,

title = "MCVdb: A database for knowledge discovery in Merkel cell polyomavirus with applications in T cell immunology and vaccinology",

abstract = "Merkel Cell Polyomavirus (MCV) is associated with more than 80% of Merkel cell carcinoma (MCC), a rare but highly lethal form of skin cancer. We made use of the immunological data on MCV available through publications and databases and constructed MCV T cell Antigen Database (MCVdb). MCVdb contains 734 curated antigen entries of MCV antigenic proteins and 30 experimentally verified T cell epitopes. The data were subject to extensive quality control (redundancy elimination, error detection, and vocabulary consolidation). A set of computational tools for in-depth analysis, such as sequence comparison using BLAST search, multiple alignments of antigens, and T cell epitope conservation analysis have been integrated within the MCVdb. Predicted Class I and Class II HLA-binding peptides for 15 common HLA alleles are included in this database as putative targets. MCVdb is a unique data source providing a comprehensive list of MCV antigens and peptides. MCVdb is publicly available at http://projects.met-hilab.org/mcv/.",

keywords = "Cancer vaccine, Merkel cell carcinoma, Merkel cell polyomavirus, T cell epitope",

author = "Zhang, {Guang Lan} and DeCaprio, {James A.} and Lou Chitkushev and Keskin, {Derin B.} and Wu, {Catherine J.} and Vladimir Brusic",

note = "Publisher Copyright: {\textcopyright} 2017 IEEE.; 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 ; Conference date: 13-11-2017 Through 16-11-2017",

year = "2017",

month = dec,

day = "15",

doi = "10.1109/BIBM.2017.8217881",

language = "English",

series = "Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017",

publisher = "Institute of Electrical and Electronics Engineers Inc.",

pages = "1483--1488",

editor = "Illhoi Yoo and Zheng, {Jane Huiru} and Yang Gong and Hu, {Xiaohua Tony} and Chi-Ren Shyu and Yana Bromberg and Jean Gao and Dmitry Korkin",

booktitle = "Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017",

address = "United States",

}

Zhang, GL, DeCaprio, JA, Chitkushev, L, Keskin, DB, Wu, CJ & Brusic, V 2017, MCVdb: A database for knowledge discovery in Merkel cell polyomavirus with applications in T cell immunology and vaccinology. in I Yoo, JH Zheng, Y Gong, XT Hu, C-R Shyu, Y Bromberg, J Gao & D Korkin (eds), Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017, vol. 2017-January, Institute of Electrical and Electronics Engineers Inc., pp. 1483-1488, 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017, Kansas City, United States, 13/11/17. https://doi.org/10.1109/BIBM.2017.8217881

MCVdb: A database for knowledge discovery in Merkel cell polyomavirus with applications in T cell immunology and vaccinology. / Zhang, Guang Lan; DeCaprio, James A.; Chitkushev, Lou et al.
Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. ed. / Illhoi Yoo; Jane Huiru Zheng; Yang Gong; Xiaohua Tony Hu; Chi-Ren Shyu; Yana Bromberg; Jean Gao; Dmitry Korkin. Institute of Electrical and Electronics Engineers Inc., 2017. p. 1483-1488 (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; Vol. 2017-January).

Research output: Chapter in Book/Conference proceeding › Conference contribution › peer-review

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AU - Zhang, Guang Lan

AU - DeCaprio, James A.

AU - Chitkushev, Lou

AU - Keskin, Derin B.

AU - Wu, Catherine J.

AU - Brusic, Vladimir

PY - 2017/12/15

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N2 - Merkel Cell Polyomavirus (MCV) is associated with more than 80% of Merkel cell carcinoma (MCC), a rare but highly lethal form of skin cancer. We made use of the immunological data on MCV available through publications and databases and constructed MCV T cell Antigen Database (MCVdb). MCVdb contains 734 curated antigen entries of MCV antigenic proteins and 30 experimentally verified T cell epitopes. The data were subject to extensive quality control (redundancy elimination, error detection, and vocabulary consolidation). A set of computational tools for in-depth analysis, such as sequence comparison using BLAST search, multiple alignments of antigens, and T cell epitope conservation analysis have been integrated within the MCVdb. Predicted Class I and Class II HLA-binding peptides for 15 common HLA alleles are included in this database as putative targets. MCVdb is a unique data source providing a comprehensive list of MCV antigens and peptides. MCVdb is publicly available at http://projects.met-hilab.org/mcv/.

AB - Merkel Cell Polyomavirus (MCV) is associated with more than 80% of Merkel cell carcinoma (MCC), a rare but highly lethal form of skin cancer. We made use of the immunological data on MCV available through publications and databases and constructed MCV T cell Antigen Database (MCVdb). MCVdb contains 734 curated antigen entries of MCV antigenic proteins and 30 experimentally verified T cell epitopes. The data were subject to extensive quality control (redundancy elimination, error detection, and vocabulary consolidation). A set of computational tools for in-depth analysis, such as sequence comparison using BLAST search, multiple alignments of antigens, and T cell epitope conservation analysis have been integrated within the MCVdb. Predicted Class I and Class II HLA-binding peptides for 15 common HLA alleles are included in this database as putative targets. MCVdb is a unique data source providing a comprehensive list of MCV antigens and peptides. MCVdb is publicly available at http://projects.met-hilab.org/mcv/.

KW - Cancer vaccine

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KW - T cell epitope

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M3 - Conference contribution

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BT - Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017

A2 - Yoo, Illhoi

A2 - Zheng, Jane Huiru

A2 - Gong, Yang

A2 - Hu, Xiaohua Tony

A2 - Shyu, Chi-Ren

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PB - Institute of Electrical and Electronics Engineers Inc.

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Zhang GL, DeCaprio JA, Chitkushev L, Keskin DB, Wu CJ, Brusic V. MCVdb: A database for knowledge discovery in Merkel cell polyomavirus with applications in T cell immunology and vaccinology. In Yoo I, Zheng JH, Gong Y, Hu XT, Shyu CR, Bromberg Y, Gao J, Korkin D, editors, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Institute of Electrical and Electronics Engineers Inc. 2017. p. 1483-1488. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017). doi: 10.1109/BIBM.2017.8217881

MCVdb: A database for knowledge discovery in Merkel cell polyomavirus with applications in T cell immunology and vaccinology

Abstract

Publication series

Conference

Keywords

ASJC Scopus subject areas

UN SDGs

Access to Document

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