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。","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":null,"pages":null},"PeriodicalIF":11.5000,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"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\":null,\"pages\":null},\"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}","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}
VIS Atlas: A Database of Virus Integration Sites in Human Genome from NGS Data to Explore Integration Patterns
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/.
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.