{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T20:01:40Z","timestamp":1786046500152,"version":"3.56.0"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs that are highly abundant in the germline. One important role of piRNAs is to defend genome integrity by guiding PIWI proteins to silence transposable elements (TEs), which have a high potential to cause deleterious effects on their host. The mechanism of piRNA-mediated post-transcriptional silencing was also observed to affect mRNAs, suggesting that piRNAs might play a broad role in gene expression regulation. However, there has been no systematic report with regard to how many protein-coding genes might be targeted and regulated by piRNAs.<\/jats:p>\n               <jats:p>Results: We trained a support vector machine classifier based on a combination of Miwi CLIP-Seq-derived features and position-derived features to predict the potential targets of piRNAs on mRNAs in the mouse. Reanalysis of a published microarray dataset suggested that the expression level of the 2587 protein-coding genes predicted as piRNA targets showed significant upregulation as a whole after abolishing the slicer activity of Miwi, supporting the conclusion that they are subject to piRNA-mediated regulation.<\/jats:p>\n               <jats:p>Availability and implementation: A web version of the method called pirnaPre as well as our results for browse is available at http:\/\/www.regulatoryrna.org\/software\/piRNA\/piRNA_target_mRNA\/index.php.<\/jats:p>\n               <jats:p>Contact: \u00a0crs@sun5.ibp.ac.cn or heshunmin@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv729","type":"journal-article","created":{"date-parts":[[2015,12,18]],"date-time":"2015-12-18T01:47:31Z","timestamp":1450403251000},"page":"1170-1177","source":"Crossref","is-referenced-by-count":28,"title":["Computational identification of piRNA targets on mouse mRNAs"],"prefix":"10.1093","volume":"32","author":[{"given":"Jiao","family":"Yuan","sequence":"first","affiliation":[{"name":"1 Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology and"},{"name":"2 CAS Key Laboratory of Rna Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peng","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ya","family":"Cui","sequence":"additional","affiliation":[{"name":"2 CAS Key Laboratory of Rna Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiajia","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Geir","family":"Skogerb\u00f8","sequence":"additional","affiliation":[{"name":"2 CAS Key Laboratory of Rna Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Da-Wei","family":"Huang","sequence":"additional","affiliation":[{"name":"1 Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Runsheng","family":"Chen","sequence":"additional","affiliation":[{"name":"2 CAS Key Laboratory of Rna Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shunmin","family":"He","sequence":"additional","affiliation":[{"name":"1 Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology and"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2015,12,16]]},"reference":[{"key":"2023020112014618600_btv729-B1","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1126\/science.1146484","article-title":"The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race","volume":"318","author":"Aravin","year":"2007","journal-title":"Science"},{"key":"2023020112014618600_btv729-B2","doi-asserted-by":"crossref","first-page":"1017","DOI":"10.1016\/S0960-9822(01)00299-8","article-title":"Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline","volume":"11","author":"Aravin","year":"2001","journal-title":"Curr. 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