Advances in high-throughput profiling of RNA-binding proteins (RBPs) have resulted inCLIP-seq datasets coupled with transcriptome profiling by RNA-seq. However, analysis methods that integrate both types of data are lacking. We describe SURF, Statistical Utility for RBP Functions, for integrative analysis of large collections of CLIP-seq and RNA-seq data. We demonstrate SURF’s ability to accurately detect differential alternative transcriptional regulation events and associate them to local protein-RNA interactions. We apply SURF to ENCODE RBP compendium and carry out downstream analysis with additional reference datasets. The results of this application are browsable at http://www.statlab.wisc.edu/shiny/surf/ .

中文翻译：

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SURF：RNA-seq 和 CLIP-seq 数据集的综合分析强调了 RNA 结合蛋白对替代转录调控的复杂控制

RNA 结合蛋白 (RBP) 高通量分析的进展产生了 CLIP-seq 数据集与 RNA-seq 转录组分析相结合。然而，缺乏整合这两类数据的分析方法。我们描述了 SURF（RBP 函数的统计实用程序），用于对大量 CLIP-seq 和 RNA-seq 数据进行综合分析。我们证明了 SURF 能够准确检测差异性替代转录调控事件并将其与局部蛋白质-RNA 相互作用相关联。我们将 SURF 应用于 ENCODE RBP 纲要，并使用其他参考数据集进行下游分析。该应用程序的结果可在 http://www.statlab.wisc.edu/shiny/surf/ 上浏览。