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Many key cancer oncogenes are driven by super-enhancers, and the mutations associated with common diseases such as Alzheimer\u2019s disease are significantly enriched with super-enhancers. Super-enhancers have shown great potential for the identification of key oncogenes and the discovery of disease-associated mutational sites.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Results<\/jats:title>\n<jats:p>In this paper, we propose a new computational method called DEEPSEN for predicting super-enhancers based on convolutional neural network. The proposed method integrates 36 kinds of features. Compared with existing approaches, our method performs better and can be used for genome-wide prediction of super-enhancers. Besides, we screen important features for predicting super-enhancers.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Conclusion<\/jats:title>\n<jats:p>Convolutional neural network is effective in boosting the performance of super-enhancer prediction.<\/jats:p>\n<\/jats:sec>","DOI":"10.1186\/s12859-019-3180-z","type":"journal-article","created":{"date-parts":[[2019,12,24]],"date-time":"2019-12-24T09:02:35Z","timestamp":1577178155000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":23,"title":["DEEPSEN: a convolutional neural network based method for super-enhancer prediction"],"prefix":"10.1186","volume":"20","author":[{"given":"Hongda","family":"Bu","sequence":"first","affiliation":[]},{"given":"Jiaqi","family":"Hao","sequence":"additional","affiliation":[]},{"given":"Yanglan","family":"Gan","sequence":"additional","affiliation":[]},{"given":"Shuigeng","family":"Zhou","sequence":"additional","affiliation":[]},{"given":"Jihong","family":"Guan","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2019,12,24]]},"reference":[{"issue":"1","key":"3180_CR1","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1038\/ng.3167","volume":"47","author":"S Pott","year":"2015","unstructured":"Pott S, Lieb JD (2015) What are super-enhancers?. 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