{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:44:57Z","timestamp":1740185097653,"version":"3.37.3"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2020,7,1]],"date-time":"2020-07-01T00:00:00Z","timestamp":1593561600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DMS1620898"],"award-info":[{"award-number":["DMS1620898"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,12,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>MicroRNAs (miRNAs) are small non-coding RNAs that have been successfully identified to be differentially expressed in various cancers. However, some miRNAs were reported to be up-regulated in one subtype of a cancer but down-regulated in another, making overall associations between these miRNAs and the heterogeneous cancer non-linear. These non-linearly associated miRNAs, if identified, are thus informative for cancer subtyping.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we propose mirPLS, a Partial Linear Structure identifier for miRNA data that simultaneously identifies miRNAs of linear or non-linear associations with cancer status when non-linearly associated miRNAs can then be used for subsequent cancer subtyping. Simulation studies showed that mirPLS can identify both non-linearly and linearly outcome-associated miRNAs more accurately than the comparison methods. Using the identified non-linearly associated miRNAs much improves the cancer subtyping accuracy. Applications to miRNA data of three different cancer types suggest that the cancer subtypes defined by the non-linearly associated miRNAs identified by mirPLS are consistently more predictive of patient survival and more biological meaningful.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The R package mirPLS is available for downloading from https:\/\/github.com\/pfruan\/mirPLS.<\/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\/btaa606","type":"journal-article","created":{"date-parts":[[2020,6,22]],"date-time":"2020-06-22T11:28:01Z","timestamp":1592825281000},"page":"4902-4909","source":"Crossref","is-referenced-by-count":1,"title":["mirPLS: a partial linear structure identifier method for cancer subtyping using microRNAs"],"prefix":"10.1093","volume":"36","author":[{"given":"Peifeng","family":"Ruan","sequence":"first","affiliation":[{"name":"Department of Statistics, Columbian College of Arts and Sciences, The George Washington University , Washington, DC 20052, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuang","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Mailman School of Public Health, Columbia University , New York, NY 10032, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hua","family":"Liang","sequence":"additional","affiliation":[{"name":"Department of Statistics, Columbian College of Arts and Sciences, The George Washington University , Washington, DC 20052, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,7,1]]},"reference":[{"key":"2023062504242860500_btaa606-B1","doi-asserted-by":"crossref","first-page":"1327","DOI":"10.1016\/j.cell.2017.05.046","article-title":"Comprehensive and integrative genomic characterization of hepatocellular carcinoma","volume":"169","author":"Ally","year":"2017","journal-title":"Cell"},{"key":"2023062504242860500_btaa606-B2","doi-asserted-by":"crossref","first-page":"F602","DOI":"10.1152\/ajprenal.00727.2010","article-title":"microRNAs in kidneys: biogenesis, regulation, and pathophysiological roles","volume":"300","author":"Bhatt","year":"2011","journal-title":"Am. 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