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| Status |
Public on Aug 07, 2012 |
| Title |
Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
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 MOV10, 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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| Overall design |
The data comprises one MOV10 PAR-CLIP data file and one nuclear RNA-seq file
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| Contributor(s) |
Sievers C, Paro R |
| Citation(s) |
22844102 |
| Submission date |
Apr 23, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Cem Sievers |
| E-mail(s) |
cem.sievers@bsse.ethz.ch
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| Organization name |
ETH Zurich
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| Street address |
Mattenstrasse
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| City |
Basel |
| ZIP/Postal code |
4057 |
| Country |
Switzerland |
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| Platforms (2) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA161009 |
| SRA |
SRP012463 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE37524_RAW.tar |
1.8 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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