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  PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs

Marsico, A., Huska, M., Lasserre, J., Hu, H., Vucicevic, D., Musahl, A., et al. (2013). PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs. Genome Biology, 14(8), R84-R84. doi:10.1186/gb-2013-14-8-r84.

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Item Permalink: https://hdl.handle.net/11858/00-001M-0000-0019-0B37-0 Version Permalink: https://hdl.handle.net/11858/00-001M-0000-0019-0B39-C
Genre: Journal Article

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 Creators:
Marsico, Annalisa1, Author           
Huska, Matthew2, Author           
Lasserre, Julia1, Author           
Hu, Haiyang3, Author
Vucicevic, Dubravka4, Author           
Musahl, Anne4, Author           
Ørom, Ulf Andersson4, Author           
Vingron, Martin5, Author           
Affiliations:
1Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, Ihnestr. 73, 14195 Berlin, Germany, ou_1433547              
2IMPRS for Computational Biology and Scientific Computing - IMPRS-CBSC (Kirsten Kelleher), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, Ihnestr. 73, 14195 Berlin, Germany, ou_1479666              
3Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , 320 Yue Yang Road, 200031 Shanghai, China, ou_persistent22              
4Long non-coding RNA (Ulf Andersson Ørom), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, Ihnestr. 73, 14195 Berlin, Germany, ou_1479659              
5Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, Ihnestr. 73, 14195 Berlin, Germany, ou_1479639              

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Free keywords: miRNA transcriptional regulation, deepCAGE, mixture model
 Abstract: The regulation of intragenic miRNAs by their own intronic promoters is one of the open problems of miRNA biogenesis. Here, we describe PROmiRNA, a new approach for miRNA promoter annotation based on a semi-supervised statistical model trained on deepCAGE data and sequence features. We validate our results with existing annotation, PolII occupancy data and read coverage from RNA-seq data. Compared to previous methods PROmiRNA increases the detection rate of intronic promoters by 30%, allowing us to perform a large-scale analysis of their genomic features, as well as elucidate their contribution to tissue-specific regulation. PROmiRNA can be downloaded from http://promirna.molgen.mpg.de.

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Language(s): eng - English
 Dates: 2013-08-16
 Publication Status: Published online
 Pages: -
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 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1186/gb-2013-14-8-r84
ISSN: 1465-6914 (Electronic)1465-6906 (Print)
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Title: Genome Biology
Source Genre: Journal
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Publ. Info: London : BioMed Central Ltd.
Pages: - Volume / Issue: 14 (8) Sequence Number: - Start / End Page: R84 - R84 Identifier: ISSN: 1465-6906
CoNE: https://pure.mpg.de/cone/journals/resource/1000000000224390_1