{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,10,6]],"date-time":"2024-10-06T00:46:19Z","timestamp":1728175579445},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: In practice, identifying and interpreting the functional impacts of the regulatory relationships between micro-RNA and messenger-RNA is non-trivial. The sheer scale of possible micro-RNA and messenger-RNA interactions can make the interpretation of results difficult.<\/jats:p><jats:p>Results: We propose a supervised framework, pMim, built upon concepts of significance combination, for jointly ranking regulatory micro-RNA and their potential functional impacts with respect to a condition of interest. Here, pMim directly tests if a micro-RNA is differentially expressed and if its predicted targets, which lie in a common biological pathway, have changed in the opposite direction. We leverage the information within existing micro-RNA target and pathway databases to stabilize the estimation and annotation of micro-RNA regulation making our approach suitable for datasets with small sample sizes. In addition to outputting meaningful and interpretable results, we demonstrate in a variety of datasets that the micro-RNA identified by pMim, in comparison to simpler existing approaches, are also more concordant with what is described in the literature.<\/jats:p><jats:p>Availability and implementation: This framework is implemented as an R function, pMim, in the package sydSeq available from http:\/\/www.ellispatrick.com\/r-packages.<\/jats:p><jats:p>Contact: \u00a0jean.yang@sydney.edu.au<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv220","type":"journal-article","created":{"date-parts":[[2015,4,25]],"date-time":"2015-04-25T01:51:42Z","timestamp":1429926702000},"page":"2822-2828","source":"Crossref","is-referenced-by-count":5,"title":["Inferring data-specific micro-RNA function through the joint ranking of micro-RNA and pathways from matched micro-RNA and gene expression data"],"prefix":"10.1093","volume":"31","author":[{"given":"Ellis","family":"Patrick","sequence":"first","affiliation":[{"name":"1 School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Buckley","sequence":"additional","affiliation":[{"name":"2 CSIRO Mathematical & Information Sciences, Clayton South, VIC 3168, Australia and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samuel","family":"M\u00fcller","sequence":"additional","affiliation":[{"name":"1 School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David M.","family":"Lin","sequence":"additional","affiliation":[{"name":"3 Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean Y. 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