{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:36Z","timestamp":1740185136820,"version":"3.37.3"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2019,11,28]],"date-time":"2019-11-28T00:00:00Z","timestamp":1574899200000},"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 Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31970630"],"award-info":[{"award-number":["31970630"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007834","name":"Natural Science Foundation of Ningbo","doi-asserted-by":"publisher","award":["2017A610154"],"award-info":[{"award-number":["2017A610154"]}],"id":[{"id":"10.13039\/100007834","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100017553","name":"Zhejiang Key Laboratory of Pathophysiology","doi-asserted-by":"crossref","award":["201812"],"award-info":[{"award-number":["201812"]}],"id":[{"id":"10.13039\/501100017553","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Scientific Innovation Team Project of Ningbo","award":["2016C51001","2017C110019"],"award-info":[{"award-number":["2016C51001","2017C110019"]}]},{"DOI":"10.13039\/501100020738","name":"K.C.Wong Magna Fund in Ningbo University","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100020738","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Long noncoding RNA (lncRNA) has been verified to interact with other biomolecules especially protein-coding genes (PCGs), thus playing essential regulatory roles in life activities and disease development. However, the inner mechanisms of most lncRNA\u2013PCG relationships are still unclear. Our study investigated the characteristics of true lncRNA\u2013PCG relationships and constructed a novel predictor with machine learning algorithms.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We obtained the 307 true lncRNA-PCG pairs from database and found that there are significant differences in multiple characteristics between true and random lncRNA\u2013PCG sets. Besides, 3-fold cross-validation and prediction results on independent test sets show the great AUC values of LR, SVM and RF, among which RF has the best performance with average AUC 0.818 for cross-validation, 0.823 and 0.853 for two independent test sets, respectively. In case study, some candidate lncRNA\u2013PCG relationships in colorectal cancer were found and HOTAIR\u2013COMP interaction was specially exemplified. The proportion of the reported pairs in the predicted positive results was significantly higher than that in negative results (P\u2009&amp;lt;\u20090.05).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz886","type":"journal-article","created":{"date-parts":[[2019,11,26]],"date-time":"2019-11-26T12:11:54Z","timestamp":1574770314000},"page":"2025-2032","source":"Crossref","is-referenced-by-count":5,"title":["Designing a general method for predicting the regulatory relationships between long noncoding RNAs and protein-coding genes based on multi-omics characteristics"],"prefix":"10.1093","volume":"36","author":[{"given":"Yuwei","family":"Zhang","sequence":"first","affiliation":[{"name":"Department of Preventative Medicine, Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine , Ningbo, Zhejiang 315211, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tianfei","family":"Yi","sequence":"additional","affiliation":[{"name":"Department of Preventative Medicine, Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine , Ningbo, Zhejiang 315211, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huihui","family":"Ji","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine , Ningbo, Zhejiang 315211, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guofang","family":"Zhao","sequence":"additional","affiliation":[{"name":"HwaMei Hospital, University of Chinese Academy of Science , Ningbo, Zhejiang 315010, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yang","family":"Xi","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine , Ningbo, Zhejiang 315211, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Changzheng","family":"Dong","sequence":"additional","affiliation":[{"name":"Department of Preventative Medicine, Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine , Ningbo, Zhejiang 315211, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lina","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Preventative Medicine, Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine , Ningbo, Zhejiang 315211, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaohong","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Preventative Medicine, Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine , Ningbo, Zhejiang 315211, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinshun","family":"Zhao","sequence":"additional","affiliation":[{"name":"Department of Preventative Medicine, Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine , Ningbo, Zhejiang 315211, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qi","family":"Liao","sequence":"additional","affiliation":[{"name":"Department of Preventative Medicine, Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine , Ningbo, Zhejiang 315211, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,11,28]]},"reference":[{"key":"2023062312014866500_btz886-B1","doi-asserted-by":"crossref","first-page":"D991","DOI":"10.1093\/nar\/gks1193","article-title":"NCBI GEO: archive for functional genomics data sets\u2014update","volume":"41","author":"Barrett","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023062312014866500_btz886-B2","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1038\/nbt1010-1045","article-title":"The NIH Roadmap Epigenomics Mapping Consortium","volume":"28","author":"Bernstein","year":"2010","journal-title":"Nat. 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