VIS Atlas: A Database of Virus Integration Sites in Human Genome from NGS Data to Explore Integration Patterns

IF 11.5 2区生物学 Q1 GENETICS & HEREDITY

Genomics, Proteomics & Bioinformatics Pub Date : 2023-04-01 DOI:10.1016/j.gpb.2023.02.005

Ye Chen , Yuyan Wang , Ping Zhou , Hao Huang , Rui Li , Zhen Zeng , Zifeng Cui , Rui Tian , Zhuang Jin , Jiashuo Liu , Zhaoyue Huang , Lifang Li , Zheying Huang , Xun Tian , Meiying Yu , Zheng Hu

{"title":"VIS Atlas: A Database of Virus Integration Sites in Human Genome from NGS Data to Explore Integration Patterns","authors":"Ye Chen , Yuyan Wang , Ping Zhou , Hao Huang , Rui Li , Zhen Zeng , Zifeng Cui , Rui Tian , Zhuang Jin , Jiashuo Liu , Zhaoyue Huang , Lifang Li , Zheying Huang , Xun Tian , Meiying Yu , Zheng Hu","doi":"10.1016/j.gpb.2023.02.005","DOIUrl":null,"url":null,"abstract":"<div><p>Integration of oncogenic <strong>DNA viruses</strong> into the human genome is a key step in most virus-induced carcinogenesis. Here, we constructed a <strong>virus integration site</strong> (VIS) Atlas database, an extensive collection of integration breakpoints for three most prevalent oncoviruses, human papillomavirus, hepatitis B virus, and Epstein–Barr virus based on the <strong>next-generation sequencing</strong> (NGS) data, literature, and experimental data. There are 63,179 breakpoints and 47,411 junctional sequences with full annotations deposited in the VIS Atlas database, comprising 47 <strong>virus genotypes</strong> and 17 disease types. The VIS Atlas database provides (1) a genome browser for NGS breakpoint quality check, visualization of VISs, and the local genomic context; (2) a novel platform to discover <strong>integration patterns</strong>; and (3) a statistics interface for a comprehensive investigation of genotype-specific integration features. Data collected in the VIS Atlas aid to provide insights into virus pathogenic mechanisms and the development of novel antitumor drugs. The VIS Atlas database is available at <span>https://www.vis-atlas.tech/</span><svg><path></path></svg>.</p></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 2","pages":"Pages 300-310"},"PeriodicalIF":11.5000,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genomics, Proteomics & Bioinformatics","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1672022923000372","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}

引用次数: 0

Abstract

Integration of oncogenic DNA viruses into the human genome is a key step in most virus-induced carcinogenesis. Here, we constructed a virus integration site (VIS) Atlas database, an extensive collection of integration breakpoints for three most prevalent oncoviruses, human papillomavirus, hepatitis B virus, and Epstein–Barr virus based on the next-generation sequencing (NGS) data, literature, and experimental data. There are 63,179 breakpoints and 47,411 junctional sequences with full annotations deposited in the VIS Atlas database, comprising 47 virus genotypes and 17 disease types. The VIS Atlas database provides (1) a genome browser for NGS breakpoint quality check, visualization of VISs, and the local genomic context; (2) a novel platform to discover integration patterns; and (3) a statistics interface for a comprehensive investigation of genotype-specific integration features. Data collected in the VIS Atlas aid to provide insights into virus pathogenic mechanisms and the development of novel antitumor drugs. The VIS Atlas database is available at https://www.vis-atlas.tech/.

查看原文本刊更多论文

VIS图谱：从NGS数据中获取人类基因组中病毒整合位点的数据库，以探索整合模式。

将致癌DNA病毒整合到人类基因组中是大多数病毒诱导致癌的关键步骤。在这里，我们构建了一个病毒整合位点（VIS）图谱数据库，该数据库基于下一代测序（NGS）数据、文献和实验数据，广泛收集了三种最流行的肿瘤病毒，人乳头瘤病毒、乙型肝炎病毒和爱泼斯坦-巴尔病毒的整合断点。VIS图谱数据库中保存了63179个断点和47411个带完整注释的连接序列，包括47种病毒基因型和17种疾病类型。VIS Atlas数据库提供（1）用于NGS断点质量检查、VIS可视化和本地基因组上下文的基因组浏览器；（2）一个发现集成模式的新颖平台；和（3）用于全面调查基因型特异性整合特征的统计界面。VIS图谱中收集的数据有助于深入了解病毒的致病机制和新型抗肿瘤药物的开发。VIS Atlas数据库可在https://www.vis-atlas.tech/.

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Genomics, Proteomics & Bioinformatics Biochemistry, Genetics and Molecular Biology-Biochemistry

CiteScore

14.30

自引率

4.20%

发文量

844

审稿时长

61 days

期刊介绍： Genomics, Proteomics and Bioinformatics (GPB) is the official journal of the Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China. It aims to disseminate new developments in the field of omics and bioinformatics, publish high-quality discoveries quickly, and promote open access and online publication. GPB welcomes submissions in all areas of life science, biology, and biomedicine, with a focus on large data acquisition, analysis, and curation. Manuscripts covering omics and related bioinformatics topics are particularly encouraged. GPB is indexed/abstracted by PubMed/MEDLINE, PubMed Central, Scopus, BIOSIS Previews, Chemical Abstracts, CSCD, among others.