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A mixture model distinguishes active from inactive CEs using sample- and CE-specific ChIP-seq variability, improving functional interpretation and enabling identification of cancer-specific CEs. Cancer-specific CEs show the strongest per-base enhancer activities in independent sequencing assays and are summarized into fingerprint states via an R package for cross-cancer querying, exploration, and visualization.",{"@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/an-epigenomic-fingerprint-of-human-cancers-by-landscape-interrogation-of-super-enhancers-at-the-constituent-level/333164/",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/an-epigenomic-fingerprint-of-human-cancers-by-landscape-interrogation-of-super-enhancers-at-the-constituent-level/333164.png","ImageObject",300,407,{"name":42,"@type":43},"Patrick","Person",{"url":19,"name":45,"@type":46},"DocShare","Organization","application/pdf","2026-11-03","2026-09-21",true,{"@type":52,"interactionType":53,"userInteractionCount":55},"InteractionCounter",{"@type":54},"ViewAction",7,{"@type":57,"mainEntity":58},"FAQPage",[59,65,69],{"name":60,"@type":61,"acceptedAnswer":62},"What problem does the study address about super enhancers?","Question",{"text":63,"@type":64},"It targets the lack of pan-cancer analyses that identify cancer-specific super enhancer signatures at the constituent enhancer (CE) level.","Answer",{"name":66,"@type":61,"acceptedAnswer":67},"How are active and inactive constituent enhancers distinguished?",{"text":68,"@type":64},"The study uses a mixture model on H3K27Ac ChIP-seq to discriminate active CEs from inactive ones by accounting for ChIP-seq variabilities between cancer samples and across CEs.",{"name":70,"@type":61,"acceptedAnswer":71},"What evidence supports that cancer-specific CEs are biologically meaningful?",{"text":72,"@type":64},"Cancer-specific CEs show the strongest per-base enhancer activities in independent enhancer sequencing assays, indicating their importance for critical SE signatures.","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},333164,1790322919,{"code":4,"msg":82,"data":83},"success",[84,88,92,96,101,106,110,114,119,122,126],{"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":55,"doc_module":4,"doc_module_name":25,"category_name":107,"show_sort_weight":108,"slug":109},"Healthcare",40,"healthcare",{"id":111,"doc_module":4,"doc_module_name":25,"category_name":29,"show_sort_weight":112,"slug":113},8,30,"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":111,"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":139,"language":140,"language_code":8,"site_id":7,"html_lang":8,"table_of_contents":141,"faqs":142,"seo_title":143,"seo_description":12,"update_tm":144,"read_time":145,"preview_page_count":4},549758146520,"https://ap-avatar.wpscdn.com/avatar/80002397d8c0411e94?_k=1775819394049821470","PLOS COMPUTATIONAL BIOLOGY  \nOPEN ACCESS  \nCitation: Liu X, Gillis N, Jiang C, McCofie A, Shaw TI, Tan A-C, et al. (2024) An Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level. PLoS Comput Biol 20(2): e1011873 . [https://doi.org/](https://doi.org/)[ ](https://doi.org/)[10.1371/journal.pcbi.1011873](10.1371/journal.pcbi.1011873)  \n[Editor:](Editor: Ilya Ioshikhes)[ Ilya Ioshikhes](Editor: Ilya Ioshikhes), CANADA  \nReceived: July 11, 2023  \nAccepted: January 30, 2024  \nPublished: February 9, 2024  \nPeer Review History: PLOS recognizes the benefits of transparency in the peer review process; therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. The editorial history of this article is available here: [https://doi.org/10.1371/journal.pcbi.101](https://doi.org/10.1371/journal.pcbi.101)1873  \nCopyright: © 2024 Liu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.  \nData Availability Statement: ChIP-seq data in this study were obtained from Gene Expression Omnibus (GEO) with accession ID GSE143653 . Other public data were summarized in S1 Table. All analysis code in this manuscript were documented  \nRESEARCH ARTICLE  \nAn Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level  \nXiang Liu1, Nancy Gillis2, Chang Jiang3, Anthony McCofie1, Timothy I. Shaw1, AikChoon Tan4, Bo Zhao5, Lixin Wan3, Derek R. Duckett6, Mingxiang Teng1 *  \n1 Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida, United States of America, 2 Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida, United States of America, 3 Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida, United States of America, 4 Department of Oncological Sciences, Huntsman Cancer Institute, The University of Utah, Salt Lake City, Utah, United States of America, 5 Division of Infectious Disease, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America,  \n6 Department of Drug Discovery, Moffitt Cancer Center, Tampa, Florida, United States of America  \n* [mingxiang.teng@moffitt.org](mingxiang.teng@moffitt.org)  \nAbstract  \nSuper enhancers (SE), large genomic elements that activate transcription and drive cell identity, have been found with cancer-specific gene regulation in human cancers. Recent studies reported the importance of understanding the cooperation and function of SE internal components, i.e. , the constituent enhancers (CE) . However, there are no pan-cancer studies to identify cancer-specific SE signatures at the constituent level. Here, by revisiting pan-cancer SE activities with H3K27Ac ChIP-seq datasets, we report fingerprint SE signatures for 28 cancer types in the NCI-60 cell panel. We implement a mixture model to discriminate active CEs from inactive CEs by taking into consideration ChIP-seq variabilities between cancer samples and across CEs. We demonstrate that the model-based estimation of CE states provides improved functional interpretation of SE-associated regulation. We identify cancer-specific CEs by balancing their active prevalence with their capability of encoding cancer type identities. We further demonstrate that cancer-specific CEs have the strongest per-base enhancer activities in independent enhancer sequencing assays, suggesting their importance in understanding critical SE signatures. We summarize fingerprint SEs based on the cancer-specific statuses of their component CEs and build an easy-touse R package to facilitate the query, exploration, and visualization of fingerprint SEs across cancers.  \nAuthor summary  \nSuper enhancers are larg","cbCainE6QV0HU4Ts","https://ap.wps.com/l/cbCainE6QV0HU4Ts","pdf",2484297,18,"English","# Abstract\n## Super enhancer and constituent enhancer background\n## Modeling approach for active versus inactive CEs\n## Cancer-specific CE identification and functional interpretation\n## Validation with independent enhancer sequencing assays\n## Fingerprint summary and R package for exploration","[{\"question\":\"What problem does the study address about super enhancers?\",\"answer\":\"It targets the lack of pan-cancer analyses that identify cancer-specific super enhancer signatures at the constituent enhancer (CE) level.\"},{\"question\":\"How are active and inactive constituent enhancers distinguished?\",\"answer\":\"The study uses a mixture model on H3K27Ac ChIP-seq to discriminate active CEs from inactive ones by accounting for ChIP-seq variabilities between cancer samples and across CEs.\"},{\"question\":\"What evidence supports that cancer-specific CEs are biologically meaningful?\",\"answer\":\"Cancer-specific CEs show the strongest per-base enhancer activities in independent enhancer sequencing assays, indicating their importance for critical SE signatures.\"}]","An Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level | PDF",1790001218,45]