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  Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MoV10PAR-CLIP data

Sievers, C., Schlumpf, T., Sawarkar, R., Comoglio, F., & Paro, R. (2012). Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MoV10PAR-CLIP data. Nucleic Acids Research (London), 40, e160. doi:org/10.1093/nar/gks697.

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 Urheber:
Sievers, Cem1, Autor
Schlumpf, Tommy1, Autor
Sawarkar, Ritwick2, Autor           
Comoglio, Federico1, Autor
Paro, Renato1, Autor
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1External Organizations, ou_persistent22              
2Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society, ou_2243642              

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 Zusammenfassung: The Photo-Activatable Ribonucleoside-enhanced CrossLinking and ImmunoPrecipitation (PAR-CLIP) method was recently developed for global identification of RNAs interacting with proteins. The strength of this versatile method results from induction of specific T to C transitions at sites of interaction. However, current analytical tools do not distinguish between non-experimentally and experimentally induced transitions. Furthermore, geometric properties at potential binding sites are not taken into account. To surmount these shortcomings, we developed a two-step algorithm consisting of a non-parametric two-component mixture model and a wavelet-based peak calling procedure. Our algorithm can reduce the number of false positives up to 24% thereby identifying high confidence interaction sites. We successfully employed this approach in conjunction with a modified PAR-CLIP protocol to study the functional role of nuclear Moloney leukemia virus 10, a putative RNA helicase interacting with Argonaute2 and Polycomb. Our method, available as the R package wavClusteR , is generally applicable to any substitution-based inference problem in genomics.

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Sprache(n): eng - English
 Datum: 2012
 Publikationsstatus: Erschienen
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 Art der Begutachtung: Expertenbegutachtung
 Identifikatoren: DOI: org/10.1093/nar/gks697
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Titel: Nucleic Acids Research (London)
  Andere : Nucleic Acids Res
Genre der Quelle: Zeitschrift
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Ort, Verlag, Ausgabe: Oxford : Oxford University Press
Seiten: - Band / Heft: 40 Artikelnummer: - Start- / Endseite: e160 Identifikator: ISSN: 0305-1048
CoNE: https://pure.mpg.de/cone/journals/resource/110992357379342