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/Report/Conference proceedingConference contribution

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 languageEnglish
Title of host publicationProceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
EditorsIllhoi Yoo, Jane Huiru Zheng, Yang Gong, Xiaohua Tony Hu, Chi-Ren Shyu, Yana Bromberg, Jean Gao, Dmitry Korkin
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1483-1488
Number of pages6
Volume2017-January
ISBN (Electronic)9781509030491
DOIs
Publication statusPublished - Dec 15 2017
Event2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 - Kansas City, United States
Duration: Nov 13 2017Nov 16 2017

Other

Other2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
CountryUnited States
CityKansas City
Period11/13/1711/16/17

Fingerprint

Merkel cell polyomavirus
Immunology
T-cells
Antigens
Allergy and Immunology
Data mining
Databases
T-Lymphocytes
Epitopes
T-Lymphocyte Epitopes
Peptides
Error detection
Merkel Cell Carcinoma
Consolidation
Vocabulary
Information Storage and Retrieval
Viral Tumor Antigens
Quality control
Redundancy
Skin Neoplasms

Keywords

  • Cancer vaccine
  • Merkel cell carcinoma
  • Merkel cell polyomavirus
  • T cell epitope

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics

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 (Vol. 2017-January, pp. 1483-1488). Institute of Electrical and Electronics Engineers Inc.. 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; Keskin, Derin B.; Wu, Catherine J.; Brusic, Vladimir.

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. Vol. 2017-January Institute of Electrical and Electronics Engineers Inc., 2017. p. 1483-1488.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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. 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, 11/13/17. https://doi.org/10.1109/BIBM.2017.8217881
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 C-R, Bromberg Y, Gao J, Korkin D, editors, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Vol. 2017-January. Institute of Electrical and Electronics Engineers Inc. 2017. p. 1483-1488 https://doi.org/10.1109/BIBM.2017.8217881
Zhang, Guang Lan ; DeCaprio, James A. ; Chitkushev, Lou ; Keskin, Derin B. ; Wu, Catherine J. ; Brusic, Vladimir. / 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. Vol. 2017-January Institute of Electrical and Electronics Engineers Inc., 2017. pp. 1483-1488
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