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YY1-mediated enhancer\u2013promoter interaction is the general feature of mammalian gene control. Recently, some computational methods have been developed to characterize the interactions between DNA elements by elucidating important features of chromatin folding; however, no computational methods have been developed for identifying the YY1-mediated chromatin loops. In this study, we developed a deep learning algorithm named DeepYY1 based on word2vec to determine whether a pair of YY1 motifs would form a loop. The proposed models showed a high prediction performance (AUCs$\\ge$0.93) on both training datasets and testing datasets in different cell types, demonstrating that DeepYY1 has an excellent performance in the identification of the YY1-mediated chromatin loops. Our study also suggested that sequences play an important role in the formation of YY1-mediated chromatin loops. Furthermore, we briefly discussed the distribution of the replication origin site in the loops. Finally, a user-friendly web server was established, and it can be freely accessed at http:\/\/lin-group.cn\/server\/DeepYY1.<\/jats:p>","DOI":"10.1093\/bib\/bbaa356","type":"journal-article","created":{"date-parts":[[2020,11,5]],"date-time":"2020-11-05T12:21:29Z","timestamp":1604578889000},"source":"Crossref","is-referenced-by-count":78,"title":["DeepYY1: a deep learning approach to identify YY1-mediated chromatin loops"],"prefix":"10.1093","volume":"22","author":[{"given":"Fu-Ying","family":"Dao","sequence":"first","affiliation":[{"name":"Center for Informational Biology at the University of Electronic Science and Technology of China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hao","family":"Lv","sequence":"additional","affiliation":[{"name":"Center for Informational Biology at the University of Electronic Science and Technology of 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