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TECHNOLOGY AND CODE article

Front. Oncol.
Sec. Molecular and Cellular Oncology
Volume 15 - 2025 | doi: 10.3389/fonc.2025.1539782
This article is part of the Research Topic Investigating the Interplay Between Tumor Mutations, Immune Evasion, and Targeted Therapy Resistance View all 12 articles

Virusplot: a web server for viral integration analysis and visualization

Provisionally accepted
Shanye Yin Shanye Yin 1,2*Erqiang Hu Erqiang Hu 2Jianhong An Jianhong An 2Adam J Gersten Adam J Gersten 2Nicole Wu Nicole Wu 2Nicole Kawachi Nicole Kawachi 3Jing Zhu Jing Zhu 2Gregory Rosenblatt Gregory Rosenblatt 2Stelby Augustine Stelby Augustine 4Richard V Smith Richard V Smith 4Jeffrey E Segall Jeffrey E Segall 2Harry Ostrer Harry Ostrer 2Antonio L Amelio Antonio L Amelio 5Christine H Chung Christine H Chung 6Michael B Prystowsky Michael B Prystowsky 2Thomas J Ow Thomas J Ow 2Wenjun Deng Wenjun Deng 7
  • 1 Albert Einstein College of Medicine, New York City, United States
  • 2 Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, United States
  • 3 The University of Texas at Austin, Austin, Texas, United States
  • 4 Department of Otorhinolaryngology Head and Neck Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York, United States
  • 5 Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, United States
  • 6 Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, United States
  • 7 Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States

The final, formatted version of the article will be published soon.

    The integration of viral DNA into the human genome is a critical event in the pathogenesis of various cancers. This process leads to genomic instability, disrupts cellular regulatory mechanisms, and activates oncogenes or inactivates tumor suppressor genes. Despite significant advancements in genome sequencing technologies, there remains a notable lack of computational tools, particularly web-based applications, specifically designed for viral integration analysis and visualization. To address this gap, we present virusPlot, a web server with the following functional modules: (i) automatic retrieval of virus genome sequences and their annotation; (ii) visualization of virus integration locations and read counts through a graphical representation that links viral and host genome integration sites, facilitating the interpretation of integration patterns; (iii) analysis of virus integration hotspots using Fisher's exact test; and (iv) integration of various functions into an interactive web platform via shinyapp. VirusPlot efficiently processes and visualizes integration data from viruses and host genomes, providing researchers with an intuitive and user-friendly analytical tool that simplifies the complexity of virus integration analysis.

    Keywords: viral integration, genomic visualization, Hotspot analysis, Computational Biology, Bioinformatics tool, host-virus interaction

    Received: 04 Dec 2024; Accepted: 31 Jan 2025.

    Copyright: © 2025 Yin, Hu, An, Gersten, Wu, Kawachi, Zhu, Rosenblatt, Augustine, Smith, Segall, Ostrer, Amelio, Chung, Prystowsky, Ow and Deng. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Shanye Yin, Albert Einstein College of Medicine, New York City, United States

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.