The prediction of tumor and normal tissues based on the DNA methylation values of ten key sites |
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| Affiliation: | 1. Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China;2. The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010070, China;3. Inner Mongolia key laboratory of gene regulation of the metabolic disease, Department of Clinical Medical Research Center, Inner Mongolia People''s Hospital, Hohhot 010010, China;1. Institute of Gene Biology RAS, 119334 Moscow, Russia;2. Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, 119334 Moscow, Russia;3. Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia;4. Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia;1. Department of Gastroenterology, Peking University Third Hospital, 49 North Garden Road, Beijing, China;2. Beijing Key Laboratory of Helicobacter pylori Infection and Upper Gastrointestinal Diseases, Peking University Third Hospital, 49 North Garden Road, Beijing, China;3. Department of Pathology, School of Basic Medical Science, Peking University Third Hospital, Peking University Health Science Center, 49 North Garden Road, Beijing, China;1. Institute of Life Sciences, Bhubaneswar 751023, India;2. Regional Centre for Biotechnology, Faridabad 121001, India;3. School of Biotechnology, KIIT University, Bhubaneswar 751024, India;1. Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada;2. Department of Pharmacology & Toxicology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada;3. Department of Pharmacology & Toxicology, Faculty of Pharmacy, Tanta University, Tanta, Egypt |
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| Abstract: | Abnormal DNA methylation can alter the gene expression to promote or inhibit tumorigenesis in colon adenocarcinoma (COAD). However, the finding important genes and key sites of abnormal DNA methylation which result in the occurrence of COAD is still an eventful task. Here, we studied the effects of DNA methylation in the 12 types of genomic features on the changes of gene expression in COAD, the 10 important COAD-related genes and the key abnormal DNA methylation sites were identified. The effects of important genes on the prognosis were verified by survival analysis. Moreover, it was shown that the important genes were participated in cancer pathways and were hub genes in a co-expression network. Based on the DNA methylation levels in the ten sites, the least diversity increment algorithm for predicting tumor tissues and normal tissues in seventeen cancer types are proposed. The better results are obtained in jackknife test. For example, the predictive accuracies are 94.17 %, 91.28 %, 89.04 % and 88.89 %, respectively, for COAD, rectum adenocarcinoma, pancreatic adenocarcinoma and cholangiocarcinoma. Finally, by computing enrichment score of infiltrating immunocytes and the activity of immune pathways, we found that the genes are highly correlated with immune microenvironment. |
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