PT - JOURNAL ARTICLE AU - Anob M. Chakrabarti AU - Nejc Haberman AU - Arne Praznik AU - Nicholas M. Luscombe AU - Jernej Ule TI - Data Science Issues in Understanding Protein-RNA Interactions AID - 10.1101/208124 DP - 2017 Jan 01 TA - bioRxiv PG - 208124 4099 - http://biorxiv.org/content/early/2017/10/25/208124.short 4100 - http://biorxiv.org/content/early/2017/10/25/208124.full AB - An interplay of experimental and computational methods is required to achieve a comprehensive understanding of protein-RNA interactions. Crosslinking and immunoprecipitation (CLIP) identifies endogenous interactions by sequencing RNA fragments that co-purify with a selected RBP under stringent conditions. Here we focus on approaches for the analysis of resulting data and appraise the methods for peak calling, visualisation, analysis and computational modelling of protein-RNA binding sites. We advocate a combined assessment of cDNA complexity and specificity for data quality control. Moreover, we demonstrate the value of analysing sequence motif enrichment in peaks assigned from CLIP data, and of visualising RNA maps, which examine the positional distribution of peaks around regulated landmarks in transcripts. We use these to assess how variations in CLIP data quality, and in different peak calling methods, affect the insights into regulatory mechanisms. We conclude by discussing future opportunities for the computational analysis of protein-RNA interaction experiments.