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Data Science Issues in Understanding Protein-RNA Interactions

Chakrabarti, A; Haberman, N; Praznik, A; Luscombe, N; Ule, J; (2018) Data Science Issues in Understanding Protein-RNA Interactions. Annual Review of Biomedical Data Science , 1 pp. 235-261. 10.1146/annurev-biodatasci-080917-013525. Green open access

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Abstract

An interplay of experimental and computational methods is required to achieve a comprehensive understanding of protein–RNA interactions. UV crosslinking and immunoprecipitation (CLIP) identifies endogenous interactions by sequencing RNA fragments that copurify with a selected RNA-binding protein under stringent conditions. Here we focus on approaches for the analysis of the resulting data and appraise the methods for peak calling, visualization, analysis, and computational modeling of protein–RNA binding sites. We advocate that the sensitivity and specificity of data be assessed in combination for computational quality control. Moreover, we demonstrate the value of analyzing sequence motif enrichment in peaks assigned from CLIP data and of visualizing 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.

Type: Article
Title: Data Science Issues in Understanding Protein-RNA Interactions
Open access status: An open access version is available from UCL Discovery
DOI: 10.1146/annurev-biodatasci-080917-013525
Publisher version: https://doi.org/10.1146/annurev-biodatasci-080917-...
Language: English
Additional information: This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions.
Keywords: RNA-binding protein, ribonucleoprotein complexes, CLIP, peak calling, data quality, RNA map
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology > Department of Neuromuscular Diseases
URI: https://discovery.ucl.ac.uk/id/eprint/10066966
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