Site identification in high-throughput RNA-protein interaction data

Uren, P. J., Bahrami-Samani, E., Burns, S. C., Qiao, M., Karginov, F. V., Hodges, E., Hannon, G. J., Sanford, J. R., Penalva, L. O. F., Smith, A. D. (2012) Site identification in high-throughput RNA-protein interaction data. Bioinformatics, 28 (23). pp. 3013-3020. ISSN 13674803 (ISSN)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/23024010
DOI: 10.1093/bioinformatics/bts569

Abstract

Motivation: Post-transcriptional and co-transcriptional regulation is a crucial link between genotype and phenotype. The central players are the RNA-binding proteins, and experimental technologies [such as cross-linking with immunoprecipitation-(CLIP-) and RIP-seq] for probing their activities have advanced rapidly over the course of the past decade. Statistically robust, flexible computational methods for binding site identification from high-throughput immunoprecipitation assays are largely lacking however.Results: We introduce a method for site identification which provides four key advantages over previous methods: (i) it can be applied on all variations of CLIP and RIP-seq technologies, (ii) it accurately models the underlying read-count distributions, (iii) it allows external covariates, such as transcript abundance (which we demonstrate is highly correlated with read count) to inform the site identification process and (iv) it allows for direct comparison of site usage across cell types or conditions. © The Author 2012. Published by Oxford University Press. All rights reserved.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > RNA regulation
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > RNA binding protein
CSHL Authors:
Communities: CSHL Post Doctoral Fellows
CSHL labs > Hannon lab
CSHL Cancer Center Program > Cancer Genetics
Depositing User: Matt Covey
Date: 2012
Date Deposited: 09 Jan 2013 16:13
Last Modified: 15 Oct 2015 15:14
PMCID: PMC3509493
Related URLs:
URI: http://repository.cshl.edu/id/eprint/26412

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