[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"doc-seo-367045-105":3,"detail-sidebar-cat-0-en-105":81,"doc-detail-367045-en":130},{"code":4,"msg":5,"data":6},0,"ok",{"site_id":7,"language":8,"slug":9,"title":10,"keywords":11,"description":12,"schema_data":13,"social_meta":74,"head_meta":76,"extra_data":78,"updated_unix":80},105,"en","the-mirna-mrna-regulatory-network-in-human-hepatocellular-carcinoma-by-transcriptomic-analysis-from-geo","The miRNA-mRNA Regulatory Network in Human Hepatocellular Carcinoma by Transcriptomic Analysis From GEO","","Bioinformatics analysis of hepatocellular carcinoma (HCC) expression profiles supports understanding of molecular mechanisms and discovery of diagnostic and therapeutic targets. The study analyzed GEO datasets and miRNA expression profiles using R to identify differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRs). Common DEGs were mapped into a STRING/Cytoscape PPI network to determine hub genes, then DEmiRs targets were predicted with the multimir package to build DEmiRs–hub gene networks.",{"@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/healthcare/","Healthcare",3,{"item":32,"name":10,"@type":21,"position":33},"https://docshare.wps.com/document/the-mirna-mrna-regulatory-network-in-human-hepatocellular-carcinoma-by-transcriptomic-analysis-from-geo/367045/",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/the-mirna-mrna-regulatory-network-in-human-hepatocellular-carcinoma-by-transcriptomic-analysis-from-geo/367045.png","ImageObject",300,407,{"name":42,"@type":43},"Logic","Person",{"url":19,"name":45,"@type":46},"DocShare","Organization","application/pdf","2026-10-29","2026-09-23",true,{"@type":52,"interactionType":53,"userInteractionCount":55},"InteractionCounter",{"@type":54},"ViewAction",9,{"@type":57,"mainEntity":58},"FAQPage",[59,65,69],{"name":60,"@type":61,"acceptedAnswer":62},"What was the study’s main objective for hepatocellular carcinoma (HCC)?","Question",{"text":63,"@type":64},"To analyze GEO-derived expression profile datasets to identify differentially expressed genes and miRNAs, and to reveal the miRNA–mRNA regulatory network relevant to HCC biology.","Answer",{"name":66,"@type":61,"acceptedAnswer":67},"How were key genes and interactions identified in the analysis?",{"text":68,"@type":64},"Common DEGs were used to construct a PPI network using STRING and Cytoscape, and hub genes were identified from this network.",{"name":70,"@type":61,"acceptedAnswer":71},"What approach was used to connect differentially expressed miRNAs (DEmiRs) with their target genes?",{"text":72,"@type":64},"The multimir package predicted target genes for DEmiRs, enabling construction of a DEmiRs–hub gene network.","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},367045,1790240379,{"code":4,"msg":82,"data":83},"success",[84,88,92,96,101,106,110,115,119,122,126],{"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":29,"show_sort_weight":108,"slug":109},7,40,"healthcare",{"id":111,"doc_module":4,"doc_module_name":25,"category_name":112,"show_sort_weight":113,"slug":114},8,"Research & Report",30,"research-report",{"id":55,"doc_module":4,"doc_module_name":25,"category_name":116,"show_sort_weight":117,"slug":118},"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":107,"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":127,"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},1099513958762,"https://ap-avatar.wpscdn.com/avatar/1000023916a998db790?x-image-process=image/resize,m_fixed,w_180,h_180&k=1784791008015729253","Cancer Reports  \nORIGINAL ARTICLE  OPEN ACCESS   \nThe miRNA-mRNA Regulatory Network in Human Hepatocellular Carcinoma by Transcriptomic Analysis From GEO  \nRazieh Heidari1,2  | Vahideh Assadollahi3  | Seyedeh Negar Marashi2  | Fatemeh Elahian2,4  | Seyed Abbas Mirzaei2,5   \n1Cancer Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran | 2Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran | 3Department of Tissue Engineering & Applied Cell Sciences, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran | 4Advanced Technology Cores, Baylor College of Medicine, Texas, USA | 5Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran  \nCorrespondence: Seyed Abbas Mirzaei ([mirzaei.a@skums.ac.ir](mirzaei.a@skums.ac.ir); [dr_amirzaei@yahoo.com](dr_amirzaei@yahoo.com))  \nReceived: 27 July 2024 | Revised: 3 October 2024 | Accepted: 12 December 2024  \nFunding: This study was supported by a grant from Shahrekord University of Medical Sciences for financial support (SKUMS-7370) .  \nKeywords: bioinformatics | biomarker | HCC | hepatocellular carcinoma | microarray | microRNA  \nABSTRACT  \nBackground: Bioinformatics analysis of hepatocellular carcinoma (HCC) expression profiles can aid in understanding its molecular mechanisms and identifying new targets for diagnosis and treatment.  \nAim: In this study, we analyzed expression profile datasets and miRNA expression profiles related to HCC from the GEO using R software to detect differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRs) .  \nMethods and results: Common DEGs were identified, and a PPI network was constructed using the STRING database and Cytoscape software to identify hub genes. The reduced levels of tumor suppressor miRNAs or down regulated DEmiRs maybe increased levels of oncogenes, the oncomirs or up regulated DEmiRs may be decreased levels of tumor suppressor genes in cancerous cells. According to this strategy, increased and decreased DEGs, also increased and decreased DEmiRs were selected. The multimir package was employed to predict target genes for DEmiRs then DEmiRs-hub gene network created. We identified approximately 1000 overlapping DEGs and 60 DEmiRs. Hub genes included RRM2, MELK, KIF11, KIF23, NCAPG, DLGAP5, BUB1B, AURKB, CCNB1, KIF20A, CCNA2, TTK, PBK, TOP2A, CDK1, MAD2L1, BIRC5, ASPM, CDCA8, and CENPF, all associated with significantly worse survival in HCC. miR-224, miR-24, miR-182, miRNA-1-3p, miR-30a, miR-27a, and miR-214 were identified as important DEmiRs with targeting more than six hub genes.  \nConclusion: Generally, our findings offer insight into the interaction of hub genes and miRNAs in the development of HCC by bioinformatics analysis, information that may prove useful in identifying biomarkers and therapeutic targets in HCC.  \n\n| Abbreviations: BP, biological process; CC, cellular component; CRC, colorectal cancer; DEGs, differentially expressed genes; DEmiR, differentially expressed miRNA; FC, fold-change; GEO, gene expression omnibus; GO, gene ontology; HCC, hepatocellular carcinoma; HR, hazard ratio; KEGG, Kyoto encyclopedia of genes and genomes; lncRNA, long non-coding RNA; MF, molecular function; miRNA, microRNA; ncRNA, non-coding RNA; PPI, protein–protein interaction; STRING, search tool for interacting genes. |\n| --- |\n| This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.\u003Cbr>© 2025 The Author(s). Cancer Reports published by Wiley Periodicals LLC. |\n\nCancer Reports, 2025; 8:e70098 1 of 19  \n[https://doi.org/10.1002/cnr2.70098](https://doi.org/10.1002/cnr2.70098)  \n1 | Introduction  \nCancer, a deadly disease, arises from disruptio","cbCaitmoA9X71xVM","https://ap.wps.com/l/cbCaitmoA9X71xVM","pdf",6365566,"English","# Abstract\n## Background\n## Aim\n## Methods and results\n## Conclusion\n# Introduction\n## Clinical challenge in HCC\n## Role of miRNAs in tumor biology\n## Need for non-invasive biomarkers","[{\"question\":\"What was the study’s main objective for hepatocellular carcinoma (HCC)?\",\"answer\":\"To analyze GEO-derived expression profile datasets to identify differentially expressed genes and miRNAs, and to reveal the miRNA–mRNA regulatory network relevant to HCC biology.\"},{\"question\":\"How were key genes and interactions identified in the analysis?\",\"answer\":\"Common DEGs were used to construct a PPI network using STRING and Cytoscape, and hub genes were identified from this network.\"},{\"question\":\"What approach was used to connect differentially expressed miRNAs (DEmiRs) with their target genes?\",\"answer\":\"The multimir package predicted target genes for DEmiRs, enabling construction of a DEmiRs–hub gene network.\"}]","The miRNA-mRNA Regulatory Network in Human Hepatocellular Carcinoma by Transcriptomic Analysis From GEO | PDF",1790168998,48]