{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:07Z","timestamp":1740185107280,"version":"3.37.3"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2017,6,8]],"date-time":"2017-06-08T00:00:00Z","timestamp":1496880000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U19AI089987","U19AI082715","P50AR070594-01"],"award-info":[{"award-number":["U19AI089987","U19AI082715","P50AR070594-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Gene set analysis is a powerful tool to study the coordinative change of time-course data. However, most existing methods only model the overall change of a gene set, yet completely overlooked heterogeneous time-dependent changes within sub-sets of genes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have developed a novel statistical method, Phantom, to investigate gene set heterogeneity. Phantom employs the principle of multi-objective optimization to assess the heterogeneity inside a gene set, which also accounts for the temporal dependency in time-course data. Phantom improves the performance of gene set based methods to detect biological changes across time.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Phantom webpage can be accessed at: http:\/\/www.baylorhealth.edu\/Phantom. R package of Phantom is available at https:\/\/cran.r-project.org\/web\/packages\/phantom\/index.html.<\/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\/btx348","type":"journal-article","created":{"date-parts":[[2017,6,3]],"date-time":"2017-06-03T03:09:32Z","timestamp":1496459372000},"page":"2957-2959","source":"Crossref","is-referenced-by-count":1,"title":["Phantom: investigating heterogeneous gene sets in time-course data"],"prefix":"10.1093","volume":"33","author":[{"given":"Jinghua","family":"Gu","sequence":"first","affiliation":[{"name":"Baylor Research Institute, 3310 Live Oak St, Dallas, TX, USA"}]},{"given":"Xuan","family":"Wang","sequence":"additional","affiliation":[{"name":"Baylor Research Institute, 3310 Live Oak St, Dallas, TX, USA"}]},{"given":"Jinyan","family":"Chan","sequence":"additional","affiliation":[{"name":"Baylor Research Institute, 3310 Live Oak St, Dallas, TX, USA"}]},{"given":"Nicole E","family":"Baldwin","sequence":"additional","affiliation":[{"name":"Baylor Research Institute, 3310 Live Oak St, Dallas, TX, USA"}]},{"given":"Jacob A","family":"Turner","sequence":"additional","affiliation":[{"name":"Baylor Research Institute, 3310 Live Oak St, Dallas, TX, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,6,8]]},"reference":[{"key":"2023020206435136100_btx348-B1","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1038\/nri3642","article-title":"Democratizing systems immunology with modular transcriptional repertoire analyses","volume":"14","author":"Chaussabel","year":"2014","journal-title":"Nat. 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