title: Site identification in high-throughput RNA-protein interaction data.
abstract: BACKGROUND
  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.
  
  
  METHODS
  We have implemented our method in a software tool called Piranha. Source code and binaries, licensed under the GNU General Public License (version 3) are freely available for download from http://smithlab.usc.edu.
  
  
  BACKGROUND
  andrewds@usc.edu
  
  
  BACKGROUND
  Supplementary data available at Bioinformatics online.
authors.affiliation: Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Philip J
authors.initials: PJ
authors.lastname: Uren
authors.forename: Emad
authors.initials: E
authors.lastname: Bahrami-Samani
authors.forename: Suzanne C
authors.initials: SC
authors.lastname: Burns
authors.forename: Mei
authors.initials: M
authors.lastname: Qiao
authors.forename: Fedor V
authors.initials: FV
authors.lastname: Karginov
authors.forename: Emily
authors.initials: E
authors.lastname: Hodges
authors.forename: Gregory J
authors.initials: GJ
authors.lastname: Hannon
authors.forename: Jeremy R
authors.initials: JR
authors.lastname: Sanford
authors.forename: Luiz O F
authors.initials: LO
authors.lastname: Penalva
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Smith
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods; D057809:HEK293 Cells; D006367:HeLa Cells; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D012313:RNA / Q000235:genetics; D016601:RNA-Binding Proteins / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D016601:RNA-Binding Proteins; D012313:RNA