{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,8]],"date-time":"2025-10-08T16:35:12Z","timestamp":1759941312921},"reference-count":0,"publisher":"Oxford University Press (OUP)","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2004,8,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Aberrant DNA methylation is common in cancer. DNA methylation profiles differ between tumor types and subtypes and provide a powerful diagnostic tool for identifying clusters of samples and\/or genes. DNA methylation data obtained with the quantitative, highly sensitive MethyLight technology is not normally distributed; it frequently contains an excess of zeros. Established tools to analyze this type of data do not exist. Here, we evaluate a variety of methods for cluster analysis to determine which is most reliable.<\/jats:p>\n               <jats:p>Results: We introduce a Bernoulli\u2013lognormal mixture model for clustering DNA methylation data obtained using MethyLight. We model the outcomes using a two-part distribution having discrete and continuous components. It is compared with standard cluster analysis approaches for continuous data and for discrete data. In a simulation study, we find that the two-part model has the lowest classification error rate for mixture outcome data compared with other approaches. The methods are illustrated using DNA methylation data from a study of lung cancer cell lines. Compared with competing hierarchical clustering methods, the mixture model approaches have the lowest cross-validation error for detecting lung cancer subtype (non-small versus small cell). The Bernoulli\u2013lognormal mixture assigns observations to subgroups with the lowest uncertainty.<\/jats:p>\n               <jats:p>Availability: Software is available upon request from the authors.<\/jats:p>\n               <jats:p>Supplementary information: \u00a0http:\/\/www-rcf.usc.edu\/~kims\/SupplementaryInfo.html<\/jats:p>","DOI":"10.1093\/bioinformatics\/bth176","type":"journal-article","created":{"date-parts":[[2004,3,30]],"date-time":"2004-03-30T01:34:06Z","timestamp":1080610446000},"page":"1896-1904","source":"Crossref","is-referenced-by-count":56,"title":["A comparison of cluster analysis methods using DNA methylation data"],"prefix":"10.1093","volume":"20","author":[{"given":"Kimberly D.","family":"Siegmund","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter W.","family":"Laird","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ite A.","family":"Laird-Offringa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2004,3,25]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/20\/12\/1896\/48905876\/bioinformatics_20_12_1896.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/20\/12\/1896\/48905876\/bioinformatics_20_12_1896.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T16:34:24Z","timestamp":1674664464000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/20\/12\/1896\/218135"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,3,25]]},"references-count":0,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2004,8,12]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bth176","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2004,8,12]]},"published":{"date-parts":[[2004,3,25]]}}}