{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,3]],"date-time":"2026-05-03T17:20:12Z","timestamp":1777828812589,"version":"3.51.4"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2022,3,21]],"date-time":"2022-03-21T00:00:00Z","timestamp":1647820800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Science Foundation of China","doi-asserted-by":"publisher","award":["61672329"],"award-info":[{"award-number":["61672329"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Science Foundation of China","doi-asserted-by":"publisher","award":["62072290"],"award-info":[{"award-number":["62072290"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shandong Provincial Project of Education Scientific Plan","award":["SDYY18058"],"award-info":[{"award-number":["SDYY18058"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,5,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Increasing biological evidence indicated that microRNAs (miRNAs) play a vital role in exploring the pathogenesis of various human diseases (especially in tumors). Mining disease-related miRNAs is of great significance for the clinical diagnosis and treatment of diseases. Compared with the traditional experimental methods with the significant limitations of high cost, long cycle and small scale, the methods based on computing have the advantages of being cost-effective. However, although the current methods based on computational biology can accurately predict the correlation between miRNAs and disease, they can not predict the detailed association information at a fine level. We propose a knowledge-driven approach to the fine-grained prediction of disease-related miRNAs (KDFGMDA). Different from the previous methods, this method can finely predict the clear associations between miRNA and disease, such as upregulation, downregulation or dysregulation. Specifically, KDFGMDA extracts triple information from massive experimental data and existing datasets to construct a knowledge graph and then trains a depth graph representation learning model based on knowledge graph to complete fine-grained prediction tasks. Experimental results show that KDFGMDA can predict the relationship between miRNA and disease accurately, which is of far-reaching significance for medical clinical research and early diagnosis, prevention and treatment of diseases. Additionally, the results of case studies on three types of cancers, Kaplan\u2013Meier survival analysis and expression difference analysis further provide the effectiveness and feasibility of KDFGMDA to detect potential candidate miRNAs. Availability: Our work can be downloaded from https:\/\/github.com\/ShengPengYu\/KDFGMDA.<\/jats:p>","DOI":"10.1093\/bib\/bbac058","type":"journal-article","created":{"date-parts":[[2022,3,18]],"date-time":"2022-03-18T12:12:52Z","timestamp":1647605572000},"source":"Crossref","is-referenced-by-count":15,"title":["A knowledge-driven network for fine-grained relationship detection between miRNA and disease"],"prefix":"10.1093","volume":"23","author":[{"given":"Shengpeng","family":"Yu","sequence":"first","affiliation":[{"name":"School of Information Science and Engineering, Shandong Normal University, Jinan, 250358, China"}]},{"given":"Hong","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Information Science and Engineering, Shandong Normal University, Jinan, 250358, China"}]},{"given":"Tianyu","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Information Science and Engineering, Shandong Normal University, Jinan, 250358, China"}]},{"given":"Cheng","family":"Liang","sequence":"additional","affiliation":[{"name":"School of Information Science and Engineering, Shandong Normal University, Jinan, 250358, China"}]},{"given":"Jiawei","family":"Luo","sequence":"additional","affiliation":[{"name":"School of Information Science and Engineering, Hunan University, Changsha, 410082, China"}]}],"member":"286","published-online":{"date-parts":[[2022,3,21]]},"reference":[{"issue":"1","key":"2022051813172304300_ref1","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbab428","article-title":"Integration of pairwise neighbor topologies and miRNA family and cluster attributes for miRNA-disease association prediction","volume":"23","author":"Xuan","year":"2021","journal-title":"Brief Bioinform"},{"issue":"6","key":"2022051813172304300_ref2","first-page":"6","article-title":"MDA-GCNFTG: identifying miRNA-disease associations based on graph convolutional networks via graph sampling through the feature and topology 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