{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T11:31:46Z","timestamp":1740137506311,"version":"3.37.3"},"reference-count":25,"publisher":"World Scientific Pub Co Pte Ltd","issue":"04","funder":[{"DOI":"10.13039\/501100002543","name":"Pusan National University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002543","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2018,8]]},"abstract":"<jats:p>In genetic association studies, regularization methods are often used due to their computational efficiency for analysis of high-dimensional genomic data. DNA methylation data generated from Infinium HumanMethylation450 BeadChip Kit have a group structure where an individual gene consists of multiple Cytosine\u2013phosphate\u2013Guanine (CpG) sites. Consequently, group-based regularization can precisely detect outcome-related CpG sites. Representative examples are sparse group lasso (SGL) and network-based regularization. The former is powerful when most of the CpG sites within the same gene are associated with a phenotype outcome. In contrast, the latter is preferred when only a few of the CpG sites within the same gene are related to the outcome. In this paper, we propose new variable selection strategy based on a selection probability that measures selection frequency of individual variables selected by both SGL and network-based regularization. In extensive simulation study, we demonstrated that the proposed strategy can show relatively outstanding selection performance under any situation, compared with both SGL and network-based regularization. Also, we applied the proposed strategy to identify differentially methylated CpG sites and their corresponding genes from ovarian cancer data.<\/jats:p>","DOI":"10.1142\/s0219720018500105","type":"journal-article","created":{"date-parts":[[2018,4,27]],"date-time":"2018-04-27T02:20:08Z","timestamp":1524795608000},"page":"1850010","source":"Crossref","is-referenced-by-count":9,"title":["New variable selection strategy for analysis of high-dimensional DNA methylation data"],"prefix":"10.1142","volume":"16","author":[{"given":"Jiyun","family":"Choi","sequence":"first","affiliation":[{"name":"Department of Statistics, Pusan National University, Busan 46241, Korea"}]},{"given":"Kipoong","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Statistics, Pusan National University, Busan 46241, Korea"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8351-2025","authenticated-orcid":false,"given":"Hokeun","family":"Sun","sequence":"additional","affiliation":[{"name":"Department of Statistics, Pusan National University, Busan 46241, Korea"}]}],"member":"219","published-online":{"date-parts":[[2018,10,23]]},"reference":[{"issue":"1","key":"S0219720018500105BIB001","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1111\/j.2517-6161.1996.tb02080.x","volume":"58","author":"Tibshirani R","year":"1996","journal-title":"J R Stat Soc Ser B"},{"key":"S0219720018500105BIB002","doi-asserted-by":"publisher","DOI":"10.1111\/j.1467-9868.2005.00503.x"},{"key":"S0219720018500105BIB003","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp041"},{"key":"S0219720018500105BIB004","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq448"},{"key":"S0219720018500105BIB005","doi-asserted-by":"publisher","DOI":"10.1002\/gepi.20623"},{"key":"S0219720018500105BIB006","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts145"},{"key":"S0219720018500105BIB007","doi-asserted-by":"publisher","DOI":"10.1002\/sim.5694"},{"key":"S0219720018500105BIB008","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1004754"},{"key":"S0219720018500105BIB009","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx064"},{"key":"S0219720018500105BIB010","doi-asserted-by":"publisher","DOI":"10.1111\/j.1467-9868.2005.00532.x"},{"key":"S0219720018500105BIB011","doi-asserted-by":"publisher","DOI":"10.1080\/10618600.2012.681250"},{"key":"S0219720018500105BIB012","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btn081"},{"key":"S0219720018500105BIB013","doi-asserted-by":"publisher","DOI":"10.1214\/10-AOAS332"},{"key":"S0219720018500105BIB014","doi-asserted-by":"publisher","DOI":"10.1111\/j.1467-9868.2010.00740.x"},{"issue":"1","key":"S0219720018500105BIB015","first-page":"101","volume":"20","author":"J F","year":"2010","journal-title":"Stat Sin"},{"key":"S0219720018500105BIB016","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts124"},{"key":"S0219720018500105BIB017","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu049"},{"key":"S0219720018500105BIB018","doi-asserted-by":"publisher","DOI":"10.1101\/gr.103606.109"},{"key":"S0219720018500105BIB019","doi-asserted-by":"publisher","DOI":"10.1002\/gepi.20619"},{"key":"S0219720018500105BIB020","doi-asserted-by":"publisher","DOI":"10.1002\/gepi.21774"},{"issue":"59","key":"S0219720018500105BIB021","first-page":"1471","volume":"13","author":"Zhuang J","year":"2012","journal-title":"BMC Bioinf"},{"key":"S0219720018500105BIB022","doi-asserted-by":"publisher","DOI":"10.1093\/carcin\/bgp006"},{"key":"S0219720018500105BIB023","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.1401987"},{"key":"S0219720018500105BIB024","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/ddp177"},{"key":"S0219720018500105BIB025","doi-asserted-by":"publisher","DOI":"10.1158\/0008-5472.CAN-10-4291"}],"container-title":["Journal of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.worldscientific.com\/doi\/pdf\/10.1142\/S0219720018500105","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,6]],"date-time":"2024-07-06T10:00:30Z","timestamp":1720260030000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/S0219720018500105"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,8]]},"references-count":25,"journal-issue":{"issue":"04","published-online":{"date-parts":[[2018,10,23]]},"published-print":{"date-parts":[[2018,8]]}},"alternative-id":["10.1142\/S0219720018500105"],"URL":"https:\/\/doi.org\/10.1142\/s0219720018500105","relation":{},"ISSN":["0219-7200","1757-6334"],"issn-type":[{"type":"print","value":"0219-7200"},{"type":"electronic","value":"1757-6334"}],"subject":[],"published":{"date-parts":[[2018,8]]}}}