{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T19:26:26Z","timestamp":1773861986221,"version":"3.50.1"},"reference-count":55,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,10,19]],"date-time":"2021-10-19T00:00:00Z","timestamp":1634601600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31771402"],"award-info":[{"award-number":["31771402"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31970590"],"award-info":[{"award-number":["31970590"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2018YFC1604000"],"award-info":[{"award-number":["2018YFC1604000"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["2662017PY116"],"award-info":[{"award-number":["2662017PY116"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>DNA methylation is known to be the most stable epigenetic modification and has been extensively studied in relation to cell differentiation, development, X chromosome inactivation and disease. Allele-specific DNA methylation (ASM) is a well-established mechanism for genomic imprinting and regulates imprinted gene expression. Previous studies have confirmed that certain special regions with ASM are susceptible and closely related to human carcinogenesis and plant development. In addition, recent studies have proven ASM to be an effective tumour marker. However, research on the functions of ASM in diseases and development is still extremely scarce. Here, we collected 4400 BS-Seq datasets and 1598 corresponding RNA-Seq datasets from 47 species, including human and mouse, to establish a comprehensive ASM database. We obtained the data on DNA methylation level, ASM and allele-specific expressed genes (ASEGs) and further analysed the ASM\/ASEG distribution patterns of these species. In-depth ASM distribution analysis and differential methylation analysis conducted in nine cancer types showed results consistent with the reported changes in ASM in key tumour genes and revealed several potential ASM tumour-related genes. Finally, integrating these results, we constructed the first well-resourced and comprehensive ASM database for 47 species (ASMdb, www.dna-asmdb.com).<\/jats:p>","DOI":"10.1093\/nar\/gkab937","type":"journal-article","created":{"date-parts":[[2021,9,30]],"date-time":"2021-09-30T16:00:32Z","timestamp":1633017632000},"page":"D60-D71","source":"Crossref","is-referenced-by-count":29,"title":["ASMdb: a comprehensive database for allele-specific DNA methylation in diverse organisms"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7948-177X","authenticated-orcid":false,"given":"Qiangwei","family":"Zhou","sequence":"first","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China"},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China"}]},{"given":"Pengpeng","family":"Guan","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China"},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China"}]},{"given":"Zhixian","family":"Zhu","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China"},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China"}]},{"given":"Sheng","family":"Cheng","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China"},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China"}]},{"given":"Cong","family":"Zhou","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China"},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China"}]},{"given":"Huanhuan","family":"Wang","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China"},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China"}]},{"given":"Qian","family":"Xu","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China"},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China"}]},{"given":"Wing-kin","family":"Sung","sequence":"additional","affiliation":[{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China"},{"name":"Department of Computer Science, National University of Singapore, Singapore 117417, Singapore"},{"name":"Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1601-6640","authenticated-orcid":false,"given":"Guoliang","family":"Li","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China"},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China"}]}],"member":"286","published-online":{"date-parts":[[2021,10,19]]},"reference":[{"key":"2022010507352846000_B1","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1101\/gr.101907.109","article-title":"Dynamic changes in the human methylome during differentiation","volume":"20","author":"Laurent","year":"2010","journal-title":"Genome Res."},{"key":"2022010507352846000_B2","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1016\/j.molcel.2012.06.019","article-title":"DNA methylation dynamics during in vivo differentiation of blood and skin stem cells","volume":"47","author":"Bock","year":"2012","journal-title":"Mol. Cell"},{"key":"2022010507352846000_B3","doi-asserted-by":"crossref","first-page":"1350","DOI":"10.1038\/ng.471","article-title":"Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts","volume":"41","author":"Doi","year":"2009","journal-title":"Nat. Genet."},{"key":"2022010507352846000_B4","doi-asserted-by":"crossref","first-page":"784706","DOI":"10.1155\/2014\/784706","article-title":"Dynamic Alu methylation during normal development, aging, and tumorigenesis","volume":"2014","author":"Luo","year":"2014","journal-title":"Biomed. Res. Int."},{"key":"2022010507352846000_B5","doi-asserted-by":"crossref","first-page":"924","DOI":"10.1111\/acel.12349","article-title":"DNA methylation and healthy human aging","volume":"14","author":"Jones","year":"2015","journal-title":"Aging Cell"},{"key":"2022010507352846000_B6","doi-asserted-by":"crossref","first-page":"a018382","DOI":"10.1101\/cshperspect.a018382","article-title":"Genomic imprinting in mammals","volume":"6","author":"Barlow","year":"2014","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"2022010507352846000_B7","doi-asserted-by":"crossref","first-page":"952","DOI":"10.1016\/j.cell.2019.01.043","article-title":"Genomic imprinting and physiological processes in mammals","volume":"176","author":"Tucci","year":"2019","journal-title":"Cell"},{"key":"2022010507352846000_B8","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1186\/s13059-014-0522-z","article-title":"Sex differences in the genome-wide DNA methylation pattern and impact on gene expression, microRNA levels and insulin secretion in human pancreatic islets","volume":"15","author":"Hall","year":"2014","journal-title":"Genome Biol."},{"key":"2022010507352846000_B9","doi-asserted-by":"crossref","first-page":"3738","DOI":"10.1038\/s41467-018-05714-3","article-title":"Autosomal genetic variation is associated with DNA methylation in regions variably escaping X-chromosome inactivation","volume":"9","author":"Luijk","year":"2018","journal-title":"Nat. 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Clin. Endocrinol. Metab."},{"key":"2022010507352846000_B20","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1038\/ng.3805","article-title":"Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tumor tissue-of-origin mapping from plasma DNA","volume":"49","author":"Guo","year":"2017","journal-title":"Nat. Genet."},{"key":"2022010507352846000_B21","doi-asserted-by":"crossref","first-page":"1698","DOI":"10.1093\/jnci\/93.22.1698","article-title":"Loss of imprinting of insulin-like growth factor-II (IGF2) gene in distinguishing specific biologic subtypes of Wilms tumor","volume":"93","author":"Ravenel","year":"2001","journal-title":"J. Natl. 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Biotechnol."},{"key":"2022010507352846000_B38","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1186\/s12920-015-0084-2","article-title":"ASEQ: fast allele-specific studies from next-generation sequencing data","volume":"8","author":"Romanel","year":"2015","journal-title":"BMC Med Genomics"},{"key":"2022010507352846000_B39","doi-asserted-by":"crossref","first-page":"e155","DOI":"10.1093\/nar\/gkt599","article-title":"Identification of active regulatory regions from DNA methylation data","volume":"41","author":"Burger","year":"2013","journal-title":"Nucleic. Acids. Res."},{"key":"2022010507352846000_B40","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1186\/s13059-018-1510-5","article-title":"A comprehensive analysis of 195 DNA methylomes reveals shared and cell-specific features of partially methylated domains","volume":"19","author":"Salhab","year":"2018","journal-title":"Genome Biol."},{"key":"2022010507352846000_B41","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1214\/aoms\/1177730491","article-title":"On a test of whether one of two random variables is stochastically larger than the other","volume":"18","author":"Mann","year":"1947","journal-title":"Ann. Math. 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Cancer Res."},{"key":"2022010507352846000_B45","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1016\/j.yexmp.2015.06.017","article-title":"Hypermethylation of FOXD3 suppresses cell proliferation, invasion and metastasis in hepatocellular carcinoma","volume":"99","author":"He","year":"2015","journal-title":"Exp. Mol. Pathol."},{"key":"2022010507352846000_B46","doi-asserted-by":"crossref","first-page":"13520","DOI":"10.1002\/jcb.28627","article-title":"DNA methylation-based diagnostic and prognostic biomarkers of nonsmoking lung adenocarcinoma patients","volume":"120","author":"Zhang","year":"2019","journal-title":"J. Cell. Biochem."},{"key":"2022010507352846000_B47","doi-asserted-by":"crossref","first-page":"W556","DOI":"10.1093\/nar\/gkz430","article-title":"GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis","volume":"47","author":"Tang","year":"2019","journal-title":"Nucleic. Acids. 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Commun."},{"key":"2022010507352846000_B51","doi-asserted-by":"crossref","first-page":"eaaw4636","DOI":"10.1126\/scitranslmed.aaw4636","article-title":"Arginine vasopressin receptor 1a is a therapeutic target for castration-resistant prostate cancer","volume":"11","author":"Zhao","year":"2019","journal-title":"Sci. Transl. Med."},{"key":"2022010507352846000_B52","doi-asserted-by":"crossref","first-page":"9710421","DOI":"10.1155\/2020\/9710421","article-title":"Identification of potential biomarkers for thyroid cancer using bioinformatics strategy: a study based on GEO datasets","volume":"2020","author":"Shen","year":"2020","journal-title":"Biomed. Res. 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