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It integrates long-read RNA-seq from 351 samples and short-read RNA-seq from 12,469 samples across normal and cancerous tissues and cells, yielding 983,789 full-length spliced isoforms and 188,248 annotated isoforms.",{"@graph":14,"@context":73},[15,34,56],{"@type":16,"itemListElement":17},"BreadcrumbList",[18,23,27,31],{"item":19,"name":20,"@type":21,"position":22},"https://docshare.wps.com","Home","ListItem",1,{"item":24,"name":25,"@type":21,"position":26},"https://docshare.wps.com/document/","Document",2,{"item":28,"name":29,"@type":21,"position":30},"https://docshare.wps.com/document/research-report/","Research & Report",3,{"item":32,"name":10,"@type":21,"position":33},"https://docshare.wps.com/document/flibase-a-comprehensive-repository-of-full-length-isoforms-across-human-cancers-and-tissues-study/326645/",4,{"url":32,"name":10,"@type":35,"image":36,"author":41,"headline":10,"publisher":44,"fileFormat":47,"inLanguage":8,"description":12,"dateModified":48,"datePublished":49,"encodingFormat":47,"isAccessibleForFree":50,"interactionStatistic":51},"DigitalDocument",{"url":37,"@type":38,"width":39,"height":40},"https://docshare.wps.com/thumbnails/flibase-a-comprehensive-repository-of-full-length-isoforms-across-human-cancers-and-tissues-study/326645.png","ImageObject",300,407,{"name":42,"@type":43},"Jiven","Person",{"url":19,"name":45,"@type":46},"DocShare","Organization","application/pdf","2026-10-29","2026-09-21",true,{"@type":52,"interactionType":53,"userInteractionCount":55},"InteractionCounter",{"@type":54},"ViewAction",8,{"@type":57,"mainEntity":58},"FAQPage",[59,65,69],{"name":60,"@type":61,"acceptedAnswer":62},"What is FLIBase and what problem does it address?","Question",{"text":63,"@type":64},"FLIBase is a specialized database that focuses on annotating full-length isoforms. It addresses the limitations of short-read RNA sequencing by leveraging long-read data for a more accurate transcript representation.","Answer",{"name":66,"@type":61,"acceptedAnswer":67},"How is FLIBase constructed from sequencing data?",{"text":68,"@type":64},"FLIBase integrates long-read RNA-seq data from 351 samples and short-read RNA-seq data from 12,469 samples. Full-length spliced isoforms are identified from long-read sequences and verified using short-read exon–exon splice junctions.",{"name":70,"@type":61,"acceptedAnswer":71},"What is the significance of tumor-specific RNA transcripts in this work?",{"text":72,"@type":64},"FLIBase highlights a large set of previously unannotated isoforms and tumor-specific RNA transcripts. These tumor-specific transcripts may provide immunogenic recurrent neoantigens and support tailored RNA-based diagnostic and therapeutic strategies.","https://schema.org",{"og:url":32,"og:type":75,"og:title":10,"og:site_name":45,"og:description":12},"article",{"robots":77,"canonical":32},"index,follow",{"doc_id":79,"site_id":7},326645,1790209880,{"code":4,"msg":82,"data":83},"success",[84,88,92,96,101,106,111,114,119,122,126],{"id":22,"doc_module":4,"doc_module_name":25,"category_name":85,"show_sort_weight":86,"slug":87},"Story & Novel",90,"story-novel",{"id":26,"doc_module":4,"doc_module_name":25,"category_name":89,"show_sort_weight":90,"slug":91},"Literature",80,"literature",{"id":33,"doc_module":4,"doc_module_name":25,"category_name":93,"show_sort_weight":94,"slug":95},"Exam",70,"exam",{"id":97,"doc_module":4,"doc_module_name":25,"category_name":98,"show_sort_weight":99,"slug":100},5,"Comic",60,"comic",{"id":102,"doc_module":4,"doc_module_name":25,"category_name":103,"show_sort_weight":104,"slug":105},6,"Technology",50,"technology",{"id":107,"doc_module":4,"doc_module_name":25,"category_name":108,"show_sort_weight":109,"slug":110},7,"Healthcare",40,"healthcare",{"id":55,"doc_module":4,"doc_module_name":25,"category_name":29,"show_sort_weight":112,"slug":113},30,"research-report",{"id":115,"doc_module":4,"doc_module_name":25,"category_name":116,"show_sort_weight":117,"slug":118},9,"Religion & Spirituality",20,"religion-spirituality",{"id":117,"doc_module":4,"doc_module_name":25,"category_name":120,"show_sort_weight":117,"slug":121},"World Cup","world-cup",{"id":123,"doc_module":4,"doc_module_name":25,"category_name":124,"show_sort_weight":123,"slug":125},10,"Lifestyle","lifestyle",{"id":127,"doc_module":4,"doc_module_name":25,"category_name":128,"show_sort_weight":97,"slug":129},19,"General","general",{"code":4,"msg":82,"data":131},{"doc_id":79,"user_id":132,"nickname":42,"user_avatar":133,"doc_module":4,"category_id":55,"category_name":29,"doc_title":10,"doc_description":12,"doc_content":134,"file_id":135,"file_url":136,"file_type":137,"file_size":138,"view_count":55,"is_deleted":4,"is_public":22,"is_downloadable":22,"audit_status":22,"page_count":123,"language":139,"language_code":8,"site_id":7,"html_lang":8,"table_of_contents":140,"faqs":141,"seo_title":142,"seo_description":12,"update_tm":143,"read_time":144,"preview_page_count":4},1099513958607,"https://ap-avatar.wpscdn.com/avatar/100002390cf8733938c?x-image-process=image/resize,m_fixed,w_180,h_180&k=1778829742770036399","FLIBase: a comprehensive repository of full-length isoforms across human cancers and tissues  \nQili Shi1 , Xinrong Li 1 , Yizhe Liu 1 , Zhiao Chen 1 ,2 ,3 and Xianghuo He 1 ,2 ,3 , *  \n1 Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China  \n2 Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China  \n3 Shanghai Key Laboratory of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China  \n* To whom correspondence should be addressed. Tel: + 86 21 34777329; Fax: +86 21 64172585; [Email: xhhe@fudan.edu.cn](Email: xhhe@fudan.edu.cn)  \nAbstract  \nRegulatory processes at the RNA transcript level play a crucial role in generating transcriptome diversity and proteome composition in human cells, impacting both physiological and pathological states. This study introduces FLIBase ([www.FLIBase.org](www.FLIBase.org)), a specialized database that focuses on annotating full-length isoforms using long-read sequencing techniques. We collected and integrated long-read (351 samples) and short-read (12 469 samples) RNA sequencing data from diverse normal and cancerous human tissues and cells. The current version of FLIBase comprises a total of 983 789 full-length spliced isoforms, identified through long-read sequences and verified using short-read exon–exon splice junctions. Of these, 188 248 isoforms have been annotated, while 795 541 isoforms remain unannotated. By overcoming the limitations of short-read RNA sequencing methods, FLIBase provides an accurate and comprehensive representation of full-length transcripts. These comprehensive annotations empower researchers to undertake various downstream analyses and investigations. Importantly, FLIBase exhibits a significant advantage in identifying a substantial number of previously unannotated isoforms and tumor-specific RNA transcripts. These tumor-specific RNA transcripts have the potential to serve as a source of immunogenic recurrent neoantigens. This remarkable discovery holds tremendous promise for advancing the development of tailored RNA-based diagnostic and therapeutic strategies for various types of human cancer.  \nGraphical abstract  \nIntroduction  \nThe regulation of transcriptome diversity and proteome composition in human cells involves a range of RNA-level regulatory processes (1,2) . These processes, including selectable transcription start sites (TSSs) (3), splicing (4) and polyadenylation (polyA) sites (5), play a crucial role in generating a diverse array of messenger RNA (mRNA) and protein isoforms with distinct structures and functions. Advances in high-throughput RNA sequencing (RNA-seq) and computational methods have greatly facilitated the analysis of transcript changes and the discovery of new transcripts in both normal physiological and pathological states (6,7) .  \nOne notable study by Demircioglu etal. utilized The Cancer Genome Atlas (TCGA) RNA-seq data to identify a significant number of cancer-associated TSSs and promoters (3). Another study conducted by Hu et al. involved reference-based transcript assembly using RNA-seq data obtained from over 1000 cancer cell lines. The findings of this study unveiled numerous transcripts that were previously unidentified (8). Importantly, specific isoform switches have been observed in various diseases, including human cancer. Tumor-preferring transcripts can promote cancer development and progression, making them attractive targets for cancer therapy. For instance, in hepatocellular carcinoma, the short isoform of BIN1 is ex-  \nReceived: July 13, 2023. Revised: August 14, 2023. Editorial Decision: August 28, 2023. Accepted: August 31, 2023 © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.  \nThis is an Open Access article distributed under the terms of the Creative Commons Attri","cbCair6xCH2NAyN5","https://ap.wps.com/l/cbCair6xCH2NAyN5","pdf",1765206,"English","# Abstract\n# Introduction\n## Transcriptome diversity and RNA-level regulation\n## Related studies and tumor-specific isoforms","[{\"question\":\"What is FLIBase and what problem does it address?\",\"answer\":\"FLIBase is a specialized database that focuses on annotating full-length isoforms. It addresses the limitations of short-read RNA sequencing by leveraging long-read data for a more accurate transcript representation.\"},{\"question\":\"How is FLIBase constructed from sequencing data?\",\"answer\":\"FLIBase integrates long-read RNA-seq data from 351 samples and short-read RNA-seq data from 12,469 samples. Full-length spliced isoforms are identified from long-read sequences and verified using short-read exon–exon splice junctions.\"},{\"question\":\"What is the significance of tumor-specific RNA transcripts in this work?\",\"answer\":\"FLIBase highlights a large set of previously unannotated isoforms and tumor-specific RNA transcripts. These tumor-specific transcripts may provide immunogenic recurrent neoantigens and support tailored RNA-based diagnostic and therapeutic strategies.\"}]","FLIBase - A comprehensive repository of full-length isoforms across human cancers and tissues - study | PDF",1789974973,25]