AUTHOR=Hu Erqiang , An Jianhong , Gersten Adam J , Wu Nicole , Kawachi Nicole , Zhu Jing , Rosenblatt Gregory , Augustine Stelby , Smith Richard V. , Segall Jeffrey E , Ostrer Harry , Amelio Antonio L , Chung Christine H. , Prystowsky Michael B. , Ow Thomas J. , Deng Wenjun , Yin Shanye 

TITLE=Virusplot: a web server for viral integration analysis and visualization

JOURNAL=Frontiers in Oncology

VOLUME=Volume 15 - 2025

YEAR=2025

URL=https://www.frontiersin.org/journals/oncology/articles/10.3389/fonc.2025.1539782

DOI=10.3389/fonc.2025.1539782

ISSN=2234-943X

ABSTRACT=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.