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

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 Abstract: 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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Language(s): eng - English
 Dates: 2012
 Publication Status: Issued
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 Rev. Type: Peer
 Identifiers: DOI: org/10.1093/nar/gks697
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Title: Nucleic Acids Research (London)
  Other : Nucleic Acids Res
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press
Pages: - Volume / Issue: 40 Sequence Number: - Start / End Page: e160 Identifier: ISSN: 0305-1048
CoNE: https://pure.mpg.de/cone/journals/resource/110992357379342