{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:44:25Z","timestamp":1753875865496,"version":"3.41.2"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2023,8,25]],"date-time":"2023-08-25T00:00:00Z","timestamp":1692921600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Cancer Center Support","award":["Nos P30CA118100","P30CA240139","R01ES030993-01A1"],"award-info":[{"award-number":["Nos P30CA118100","P30CA240139","R01ES030993-01A1"]}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute, USA","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,9,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>As an important player in transcriptome regulation, microRNAs may effectively diffuse somatic mutation impacts to broad cellular processes and ultimately manifest disease and dictate prognosis. Previous studies that tried to correlate mutation with gene expression dysregulation neglected to adjust for the disparate multitudes of false positives associated with unequal sample sizes and uneven class balancing scenarios.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>To properly address this issue, we developed a statistical framework to rigorously assess the extent of mutation impact on microRNAs in relation to a permutation-based null distribution of a matching sample structure. Carrying out the framework in a pan-cancer study, we ascertained 9008 protein-coding genes with statistically significant mutation impacts on miRNAs. Of these, the collective miRNA expression for 83 genes showed significant prognostic power in nine cancer types. For example, in lower-grade glioma, 10 genes\u2019 mutations broadly impacted miRNAs, all of which showed prognostic value with the corresponding miRNA expression. Our framework was further validated with functional analysis and augmented with rich features including the ability to analyze miRNA isoforms; aggregative prognostic analysis; advanced annotations such as mutation type, regulator alteration, somatic motif, and disease association; and instructive visualization such as mutation OncoPrint, Ideogram, and interactive mRNA\u2013miRNA network.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The data underlying this article are available in MutMix, at http:\/\/innovebioinfo.com\/Database\/TmiEx\/MutMix.php.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad520","type":"journal-article","created":{"date-parts":[[2023,8,25]],"date-time":"2023-08-25T18:07:07Z","timestamp":1692986827000},"source":"Crossref","is-referenced-by-count":1,"title":["Somatic mutation effects diffused over microRNA dysregulation"],"prefix":"10.1093","volume":"39","author":[{"given":"Hui","family":"Yu","sequence":"first","affiliation":[{"name":"Department of Public Health, Sylvester Comprehensive Cancer Center, University of Miami , Miami, FL 33136, U.S.A"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Limin","family":"Jiang","sequence":"additional","affiliation":[{"name":"Department of Public Health, Sylvester Comprehensive Cancer Center, University of Miami , Miami, FL 33136, U.S.A"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chung-I","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Statistics, National Cheng Kung University , Tainan 701401, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Scott","family":"Ness","sequence":"additional","affiliation":[{"name":"Comprehensive Cancer Center, University of New Mexico , Albuquerque, NM 87109, United 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