{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T14:33:52Z","timestamp":1761489232005},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation:\u2003Systematic identification of microRNA (miRNA) targets remains a challenge. The miRNA overexpression coupled with genome-wide expression profiling is a promising new approach and calls for a new method that integrates expression and sequence information.<\/jats:p>\n               <jats:p>Results:\u2003We developed a probabilistic scoring method called targetScore. TargetScore infers miRNA targets as the transformed fold-changes weighted by the Bayesian posteriors given observed target features. To this end, we compiled 84 datasets from Gene Expression Omnibus corresponding to 77 human tissue or cells and 113 distinct transfected miRNAs. Comparing with other methods, targetScore achieves significantly higher accuracy in identifying known targets in most tests. Moreover, the confidence targets from targetScore exhibit comparable protein downregulation and are more significantly enriched for Gene Ontology terms. Using targetScore, we explored oncomir\u2013oncogenes network and predicted several potential cancer-related miRNA\u2013messenger RNA interactions.<\/jats:p>\n               <jats:p>Availability and implementation:\u2003TargetScore is available at Bioconductor: http:\/\/www.bioconductor.org\/packages\/devel\/bioc\/html\/TargetScore.html.<\/jats:p>\n               <jats:p>Contact:\u2003yueli@cs.toronto.edu or zhaolei.zhang@utoronto.ca<\/jats:p>\n               <jats:p>Supplementary information:\u2003Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt599","type":"journal-article","created":{"date-parts":[[2013,10,18]],"date-time":"2013-10-18T02:15:04Z","timestamp":1382062504000},"page":"621-628","source":"Crossref","is-referenced-by-count":34,"title":["A probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information"],"prefix":"10.1093","volume":"30","author":[{"given":"Yue","family":"Li","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, 2The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, 3Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario M5G 1L7 and 4Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada"},{"name":"1 Department of Computer Science, 2The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, 3Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario M5G 1L7 and 4Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna","family":"Goldenberg","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, 2The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, 3Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario M5G 1L7 and 4Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada"},{"name":"1 Department of Computer Science, 2The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, 3Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario M5G 1L7 and 4Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ka-Chun","family":"Wong","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, 2The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, 3Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario M5G 1L7 and 4Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada"},{"name":"1 Department of Computer Science, 2The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, 3Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario M5G 1L7 and 4Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhaolei","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, 2The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, 3Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario M5G 1L7 and 4Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada"},{"name":"1 Department of Computer Science, 2The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, 3Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario M5G 1L7 and 4Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada"},{"name":"1 Department of Computer Science, 2The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, 3Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario M5G 1L7 and 4Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,10,17]]},"reference":[{"key":"2023012710432851600_btt599-B1","doi-asserted-by":"crossref","first-page":"3049","DOI":"10.1093\/bioinformatics\/btp565","article-title":"Lost in translation: an assessment and perspective for computational microRNA target 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