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The release adds mouse eccDNA collections, introduces a motif discovery module for junction-specific pattern identification, and enhances functional prioritization via an improved scoring framework integrating multi-omic annotations. These features support flexible querying, batch downloads, visualization, and integrative analyses, enabling studies of eccDNA regulatory roles in cancer and other diseases.",{"@graph":69,"@context":122},[70,84,105],{"@type":71,"itemListElement":72},"BreadcrumbList",[73,77,79,82],{"item":74,"name":75,"@type":76,"position":8},"https://docshare.wps.com","Home","ListItem",{"item":78,"name":9,"@type":76,"position":14},"https://docshare.wps.com/document/",{"item":80,"name":40,"@type":76,"position":81},"https://docshare.wps.com/document/research-report/",3,{"item":83,"name":65,"@type":76,"position":19},"https://docshare.wps.com/document/circlebase-v2-an-eccdna-annotation-platform-across-cancers-and-species/346264/",{"url":83,"name":65,"@type":85,"image":86,"author":91,"headline":65,"publisher":94,"fileFormat":97,"inLanguage":63,"description":67,"dateModified":98,"datePublished":99,"encodingFormat":97,"isAccessibleForFree":100,"interactionStatistic":101},"DigitalDocument",{"url":87,"@type":88,"width":89,"height":90},"https://docshare.wps.com/thumbnails/circlebase-v2-an-eccdna-annotation-platform-across-cancers-and-species/346264.png","ImageObject",300,407,{"name":92,"@type":93},"Logic","Person",{"url":74,"name":95,"@type":96},"DocShare","Organization","application/pdf","2026-09-24","2026-09-22",true,{"@type":102,"interactionType":103,"userInteractionCount":8},"InteractionCounter",{"@type":104},"ViewAction",{"@type":106,"mainEntity":107},"FAQPage",[108,114,118],{"name":109,"@type":110,"acceptedAnswer":111},"What is CircleBase V2 used for?","Question",{"text":112,"@type":113},"CircleBase V2 is a resource for investigating extrachromosomal circular DNA (eccDNA) by providing curated data and functional annotations for humans and mice.","Answer",{"name":115,"@type":110,"acceptedAnswer":116},"What major data expansion does CircleBase V2 provide?",{"text":117,"@type":113},"CircleBase V2 increases eccDNA data with over 7.4 million entries covering more than 300 types of cell lines and tissues, and it adds mouse eccDNAs with over 3.6 million entries across 20+ tissues.",{"name":119,"@type":110,"acceptedAnswer":120},"How does CircleBase V2 help prioritize functionally relevant eccDNAs?",{"text":121,"@type":113},"It includes an improved functional scoring framework that integrates multi-omic annotations such as chromatin accessibility, regulatory elements, genetic variants, and chromatin interactions.","https://schema.org",{"og:url":83,"og:type":124,"og:title":65,"og:site_name":95,"og:description":67},"article",{"robots":126,"canonical":83},"index,follow",{"doc_id":128,"site_id":62},346264,1790218984,{"code":4,"msg":5,"data":131},{"doc_id":128,"user_id":132,"nickname":92,"user_avatar":133,"doc_module":4,"category_id":39,"category_name":40,"doc_title":65,"doc_description":67,"doc_content":134,"file_id":135,"file_url":136,"file_type":137,"file_size":138,"view_count":8,"is_deleted":4,"is_public":8,"is_downloadable":8,"audit_status":8,"page_count":139,"language":140,"language_code":63,"site_id":62,"html_lang":63,"table_of_contents":141,"faqs":142,"seo_title":143,"seo_description":67,"update_tm":144,"read_time":41},1099513958762,"https://ap-avatar.wpscdn.com/avatar/1000023916a998db790?x-image-process=image/resize,m_fixed,w_180,h_180&k=1784791008015729253","Nucleic Acids Research, 2026, 54, D66–D77  \n[https://doi.org/10.1093/nar/gkaf1266](https://doi.org/10.1093/nar/gkaf1266)  \nAdvance access publication date: 22 November 2025  \nDatabase issue  \nCircleBase V2: an eccDNA annotation platform across cancers and species  \nLing Wei1,2,3 ,†, Leisheng Shi1,2,3 ,†, Ning Wu4,5,6,7,†, Hongyu Zhao4,5,6,7,†, Zibaguli Wubulikasimu4,5,6,7, Keyan Liu8 , Ming Deng 1,2 , Fengbiao Mao 1,2,3 ,* , Xi Xiang9 ,* , Hongsen Bi8 ,* , Xiaolu Zhao4,5,6,7,*  \n1 Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China  \n2 Cancer Center, Peking University Third Hospital, Beijing 100191, China  \n3 Beijing Key Laboratory for Interdisciplinary Research in Gastrointestinal Oncology (BLGO), Beijing 100191, China  \n4 State Key Laboratory of Female Fertility Promotion, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China  \n5 National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China  \n6 Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China  \n7 Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China  \n8 Department of Plastic Surgery, Peking University Third Hospital, Beijing 100191, China  \n9 Scientific Research Center, Department of Urology, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518107, China  \n∗ To whom correspondence should be [addressed. Email:](addressed. Email: xiaolu@bjmu.edu.cn)[ xiaolu@bjmu.edu.cn](addressed. Email: xiaolu@bjmu.edu.cn)  \nCorrespondence may also be addressed to Hongsen Bi. Email: [bihongsen@bjmu.edu.cn](bihongsen@bjmu.edu.cn)  \nCorrespondence may also be addressed [to Xi Xiang. Email:](to Xi Xiang. Email: xiangx25@mail.sysu.edu.cn)[ xiangx25@mail.sysu.edu.cn](to Xi Xiang. Email: xiangx25@mail.sysu.edu.cn)  \nCorrespondence may also be addressed to Fengbiao Mao. Email: [fengbiaomao@bjmu.edu.cn](fengbiaomao@bjmu.edu.cn)  \n†The first four authors should be regarded as Joint First Authors.  \nAbstract  \nCircleBase V2 ([http://circlebase2.maolab.org](http://circlebase2.maolab.org)) is a comprehensive update of our previously developed database, offering a significantly expanded and functionally enhanced resource for investigating extrachromosomal circular DNA (eccDNA) in human and mouse. This version introduces several key advancements: (i) a 12-fold increase in eccDNA data, comprising over 7.4 million entries from >300 types of cell lines and tissues, providing broader coverage across diverse physiological and disease contexts; (ii) inclusion of mouse eccDNAs, with >3.6 million entries from over 20 tissues, enabling robust cross-species comparative analyses and enhancing translational research with mouse models; (iii) a dedicated motif discovery module that systematically identifies junction-specific sequence patterns, shedding light on molecular mechanisms underlying eccDNA formation; and (iv) an improved functional scoring framework that integrates multi-omic annotations, including chromatin accessibility, regulatory elements, genetic variants, and chromatin interactions, to help prioritize functionally relevant eccDNAs. Additionally, CircleBase V2 features an upgraded user interface with enhanced visualization tools, supporting flexible querying, batch downloads, and integrative analyses. Collectively, these advancements establish CircleBase V2 as an indispensable platform for uncovering the biological roles and regulatory functions of eccDNAs in cancer, development, and other diseases.  \nGraphical abstract  \nReceived: September 11, 2025. Revised: October 19, 2025. Accepted: October 20, 2025  \n© The Author(s) 2025. Published by Oxford University Press.  \nThis is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License  \n","cbCaiifmR5WnhEAa","https://ap.wps.com/l/cbCaiifmR5WnhEAa","pdf",2346257,12,"English","# Abstract\n# Introduction\n## eccDNA overview\n## eccDNA roles in cancer\n## Advances in eccDNA biogenesis and function\n# Graphical abstract\n# Publication information","[{\"question\":\"What is CircleBase V2 used for?\",\"answer\":\"CircleBase V2 is a resource for investigating extrachromosomal circular DNA (eccDNA) by providing curated data and functional annotations for humans and mice.\"},{\"question\":\"What major data expansion does CircleBase V2 provide?\",\"answer\":\"CircleBase V2 increases eccDNA data with over 7.4 million entries covering more than 300 types of cell lines and tissues, and it adds mouse eccDNAs with over 3.6 million entries across 20+ tissues.\"},{\"question\":\"How does CircleBase V2 help prioritize functionally relevant eccDNAs?\",\"answer\":\"It includes an improved functional scoring framework that integrates multi-omic annotations such as chromatin accessibility, regulatory elements, genetic variants, and chromatin interactions.\"}]","CircleBase V2 - an eccDNA annotation platform across cancers and species | PDF",1790060712]