| Chen Jinhua,Huang Xiaoting,Jin Jiaying,Ding Boyang,Zhu Ran,Li Wenyan,Liu Fenju,Yu Jiahua.Construction and application of a random forest-based classification model for DNA double-strand break induced by ionizing radiation[J].Chinese Journal of Radiological Medicine and Protection,2021,41(6):413-417 |
| Construction and application of a random forest-based classification model for DNA double-strand break induced by ionizing radiation |
| Received:October 28, 2020 |
| DOI：10.3760/cma.j.issn.0254-5098.2021.06.003 |
| KeyWords:Ionizing radiation DNA double-strand break Random forest Classification model Epigenetics |
| FundProject:国家自然科学基金（81872548） |
| Author Name | Affiliation | E-mail | | Chen Jinhua | Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection of Soochow University, Suzhou 215123, China | | | Huang Xiaoting | Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection of Soochow University, Suzhou 215123, China | | | Jin Jiaying | Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection of Soochow University, Suzhou 215123, China | | | Ding Boyang | Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection of Soochow University, Suzhou 215123, China | | | Zhu Ran | Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection of Soochow University, Suzhou 215123, China | | | Li Wenyan | Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection of Soochow University, Suzhou 215123, China | | | Liu Fenju | Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection of Soochow University, Suzhou 215123, China | | | Yu Jiahua | Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection of Soochow University, Suzhou 215123, China | yujiahua@suda.edu.cn |
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| Abstract:: |
| Objective To construct a random forest classification model of DNA double strand breaks (DSB) induced by ionizing radiation and investigate the genome-wide distribution of DSB. Methods The GRCh38 reference genome was divided into 50 kilobase fragments. Then these genomic fragments were separated into low-level or high-level regions of ionizing radiation-induced DSB according to the sequencing data of MCF-7 cells. The data of eight epigenetic features were used as input. Two thirds of the data were randomly assigned to the training set, and the rest of the data was assigned to the test set. A random forest classification model with 100 decision trees was constructed. The importance of epigenetic features in the classification model was analyzed and displayed. Results The accuracy score of the random forest classification model on the test set was 99.4%, the precision score was 98.9% and the recall score was 99.9%. The area under the receiver operating characteristic curve was 0.994. Among the eight epigenetic features, H3K36me3 and DNase markers were the most important variables. The enrichments of the two markers in DSB high-level regions were much higher than those in DSB low-level regions. Conclusions The random forest classification model could precisely predict the genome-wide levels of DSB induced by ionizing radiation in the 50 kilobase window based on epigenetic features. Analysis revealed that these DSB might primarily distribute in the actively transcribed sites in the genome. |
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