Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, Berlin, 13125, Germany.
Department of Biology, Humboldt University, Berlin, Germany.
Genome Biol. 2018 Nov 1;19(1):183. doi: 10.1186/s13059-018-1521-2.
CLIP-seq methods allow the generation of genome-wide maps of RNA binding protein - RNA interaction sites. However, due to differences between different CLIP-seq assays, existing computational approaches to analyze the data can only be applied to a subset of assays. Here, we present a probabilistic model called omniCLIP that can detect regulatory elements in RNAs from data of all CLIP-seq assays. omniCLIP jointly models data across replicates and can integrate background information. Therefore, omniCLIP greatly simplifies the data analysis, increases the reliability of results and paves the way for integrative studies based on data from different assays.
CLIP-seq 方法允许生成 RNA 结合蛋白-RNA 相互作用位点的全基因组图谱。然而，由于不同 CLIP-seq 检测方法之间的差异，现有的分析数据的计算方法只能应用于部分检测方法。在这里，我们提出了一种称为 omniCLIP 的概率模型，该模型可以从所有 CLIP-seq 检测方法的数据中检测 RNA 中的调节元件。omniCLIP 联合对重复数据进行建模，并且可以整合背景信息。因此，omniCLIP 大大简化了数据分析，提高了结果的可靠性，并为基于不同检测方法的数据的综合研究铺平了道路。
