CanVaxKB: a web-based cancer vaccine knowledgebase.

Journal: NAR cancer
PMID: 38204924

Abstract

Cancer vaccines have been increasingly studied and developed to prevent or treat various types of cancers. To systematically survey and analyze different reported cancer vaccines, we developed CanVaxKB (https://violinet.org/canvaxkb), the first web-based cancer vaccine knowledgebase that compiles over 670 therapeutic or preventive cancer vaccines that have been experimentally verified to be effective at various stages. Vaccine construction and host response data are also included. These cancer vaccines are developed against various cancer types such as melanoma, hematological cancer, and prostate cancer. CanVaxKB has stored 263 genes or proteins that serve as cancer vaccine antigen genes, which we have collectively termed 'canvaxgens'. Top three mostly used canvaxgens are PMEL, MLANA and CTAG1B, often targeting multiple cancer types. A total of 193 canvaxgens are also reported in cancer-related ONGene, Network of Cancer Genes and/or Sanger Cancer Gene Consensus databases. Enriched functional annotations and clusters of canvaxgens were identified and analyzed. User-friendly web interfaces are searchable for querying and comparing cancer vaccines. CanVaxKB cancer vaccines are also semantically represented by the community-based Vaccine Ontology to support data exchange. Overall, CanVaxKB is a timely and vital cancer vaccine source that facilitates efficient collection and analysis, further helping researchers and physicians to better understand cancer mechanisms.

Authors

  • Eliyas Asfaw
    College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA.
  • Asiyah Yu Lin
    Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
  • Anthony Huffman
    Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States.
  • Siqi Li
    Software College, Northeastern University, Shenyang 110819, China.
  • Madison George
    College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA.
  • Chloe Darancou
    College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA.
  • Madison Kalter
    College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA.
  • Nader Wehbi
    College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA.
  • Davis Bartels
    College of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA.
  • Elyse Fleck
    College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA.
  • Nancy Tran
    College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA.
  • Daniel Faghihnia
    College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA.
  • Kimberly Berke
    College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA.
  • Ronak Sutariya
    College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA.
  • Farah Reyal
    Department of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, MD 21250, USA.
  • Youssef Tammam
    Department of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, MD 21250, USA.
  • Bin Zhao
    University of Michigan Medical School, Ann Arbor, MI 48109, USA.
  • Edison Ong
    University of Michigan Medical School, Ann Arbor, MI 48109, USA.
  • Zuoshuang Xiang
    University of Michigan Medical School, Ann Arbor, MI 48109 USA.
  • Virginia He
    The College of Brown University, Brown University, Providence, RI 02912, USA.
  • Justin Song
    College of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA.
  • Andrey I Seleznev
    Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
  • Jinjing Guo
    Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
  • Yuanyi Pan
    Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
  • Jie Zheng
    State Key Laboratory of Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, Wuhan, China.
  • Yongqun He
    University of Michigan Medical School, Ann Arbor, MI 48109 USA ; Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, and Comprehensive Cancer Center, University of Michigan Medical School, 1301 MSRB III, 1150 W. Medical Dr., Ann Arbor, MI 48109 USA.

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