{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,1]],"date-time":"2025-10-01T15:27:38Z","timestamp":1759332458450,"version":"3.41.2"},"reference-count":66,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,12,7]],"date-time":"2022-12-07T00:00:00Z","timestamp":1670371200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62171166","62272212","62225109","62072095"],"award-info":[{"award-number":["62171166","62272212","62225109","62072095"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>DNA methylation within gene body and promoters in cancer cells is well documented. An increasing number of studies showed that cytosine\u2013phosphate\u2013guanine (CpG) sites falling within other regulatory elements could also regulate target gene activation, mainly by affecting transcription factors (TFs) binding in human cancers. This led to the urgent need for comprehensively and effectively collecting distinct cis-regulatory elements and TF-binding sites (TFBS) to annotate DNA methylation regulation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed a database (CanMethdb, http:\/\/meth.liclab.net\/CanMethdb\/) that focused on the upstream and downstream annotations for CpG\u2013genes in cancers. This included upstream cis-regulatory elements, especially those involving distal regions to genes, and TFBS annotations for the CpGs and downstream functional annotations for the target genes, computed through integrating abundant DNA methylation and gene expression profiles in diverse cancers. Users could inquire CpG\u2013target gene pairs for a cancer type through inputting a genomic region, a CpG, a gene name, or select hypo\/hypermethylated CpG sets. The current version of CanMethdb documented a total of 38\u00a0986\u00a0060 CpG\u2013target gene pairs (with 6\u00a0769\u00a0130 unique pairs), involving 385\u00a0217 CpGs and 18\u00a0044 target genes, abundant cis-regulatory elements and TFs for 33 TCGA cancer types. CanMethdb might help biologists perform in-depth studies of target gene regulations based on DNA methylations in cancer.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The main program is available at https:\/\/github.com\/chunquanlipathway\/CanMethdb.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac783","type":"journal-article","created":{"date-parts":[[2022,12,7]],"date-time":"2022-12-07T06:44:26Z","timestamp":1670395466000},"source":"Crossref","is-referenced-by-count":5,"title":["CanMethdb: a database for genome-wide DNA methylation annotation in cancers"],"prefix":"10.1093","volume":"39","author":[{"given":"Jianmei","family":"Zhao","sequence":"first","affiliation":[{"name":"The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China , Hengyang 421001, China"},{"name":"College of Life Sciences, Northeast Forestry University , Harbin 150038, China"},{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University , Daqing 163711, China"}]},{"given":"Fengcui","family":"Qian","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China , Hengyang 421001, China"},{"name":"School of Computer, University of South China , Hengyang 421001, China"},{"name":"The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China , Hengyang 421001, China"},{"name":"Department of Cell Biology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China , Hengyang 421001, China"}]},{"given":"Xuecang","family":"Li","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University , Daqing 163711, China"}]},{"given":"Zhengmin","family":"Yu","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China , Hengyang 421001, China"},{"name":"School of Computer, University of South China , Hengyang 421001, China"},{"name":"The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China , Hengyang 421001, China"}]},{"given":"Jiang","family":"Zhu","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University , Daqing 163711, China"},{"name":"College of Information and Computer Engineering, Northeast Forestry University , Harbin 150038, China"}]},{"given":"Rui","family":"Yu","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University , Harbin 150088, China"}]},{"given":"Yue","family":"Zhao","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University , Harbin 150088, China"}]},{"given":"Ke","family":"Ding","sequence":"additional","affiliation":[{"name":"College of Information and Computer Engineering, Northeast Forestry University , Harbin 150038, China"}]},{"given":"Yanyu","family":"Li","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University , Daqing 163711, China"}]},{"given":"Yongsan","family":"Yang","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University , Daqing 163711, China"}]},{"given":"Qi","family":"Pan","sequence":"additional","affiliation":[{"name":"Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Department of Rheumatology, Zhon gshan Hospital, Fudan University , Shanghai 200433, China"}]},{"given":"Jiaxin","family":"Chen","sequence":"additional","affiliation":[{"name":"Shenzhen Bay Laboratory, Pingshan Translational Medicine Center , Shenzhen 518118, China"}]},{"given":"Chao","family":"Song","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China , Hengyang 421001, China"},{"name":"School of Computer, University of South China , Hengyang 421001, China"},{"name":"The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China , Hengyang 421001, China"}]},{"given":"Qiuyu","family":"Wang","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China , Hengyang 421001, China"},{"name":"School of Computer, University of South China , Hengyang 421001, China"},{"name":"The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China , Hengyang 421001, China"}]},{"given":"Jian","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University , Daqing 163711, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7381-2374","authenticated-orcid":false,"given":"Guohua","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Northeast Forestry University , Harbin 150038, China"},{"name":"College of Information and Computer Engineering, Northeast Forestry University , Harbin 150038, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4700-5496","authenticated-orcid":false,"given":"Chunquan","family":"Li","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China , Hengyang 421001, China"},{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University , Daqing 163711, China"},{"name":"School of Computer, University of South China , Hengyang 421001, China"},{"name":"The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China , Hengyang 421001, China"},{"name":"Department of Cell Biology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China , Hengyang 421001, 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