HPVdb: A Data mining system for knowledge discovery in human papillomavirus with applications in T cell immunology and vaccinology

Guang Lan Zhang, Angelika Riemer, Derin B. Keskin, Lou Chitkushev, Ellis L. Reinherz, Vladimir Brusic

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

Abstract

High-risk human papilloma viruses (HPV) are the causes of many cancers, including cervical, anal, vulvar, vaginal, penile and oropharyngeal. To facilitate diagnosis, prognosis, and characterization of these cancers, we constructed the Human Papillomavirus T cell Antigen Database (HPVdb). It contains 2865 curated antigen entries of antigenic proteins derived from 18 genotypes of high-risk HPV and 18 genotypes of low-risk HPV. HPVdb also catalogs 96 verified T cell epitopes and 45 verified HLA ligands. Primary amino acid sequences of HPV antigens were collected and annotated from UniProtKB. T cell epitopes and HLA ligands were collected from data mining of scientific literature. 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, classification of HPV types based on cancer risk, and T cell epitope/HLA ligand visualization, have been integrated in HPVdb. Predicted Class I and Class II HLA binding peptides for 15 common HLA alleles are included in this database as putative targets. HPVdb is a specialized database that integrates curated data and information with tailored analysis tools to facilitate data mining to aid rational vaccine design by discovery of vaccine targets. To our best knowledge, HPVdb is a unique data source providing a comprehensive list of antigen peptides in HPV.

Original languageEnglish
Title of host publication2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013
Pages843-848
Number of pages6
DOIs
Publication statusPublished - 2013
Event2013 4th ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013 - Wshington, DC, United States
Duration: Sep 22 2013Sep 25 2013

Publication series

Name2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013

Other

Other2013 4th ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013
CountryUnited States
CityWshington, DC
Period9/22/139/25/13

Keywords

  • Human papilloma viruses
  • Immunological databases
  • T cell epitopes
  • Vaccine target discovery
  • Viral antigens

ASJC Scopus subject areas

  • Bioengineering
  • Biomedical Engineering
  • Health Informatics

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