An interactive web-based application for Comprehensive Analysis of RNAi-screen Data.
An interactive web-based application for Comprehensive Analysis of RNAi-screen Data.
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DOI：
10.1038/ncomms10578
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发表时间：
2016-02-23
影响因子：
16.6
通讯作者：
Fraser ID
中科院分区：
文献类型：
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作者：
Dutta B;Azhir A;Merino LH;Guo Y;Revanur S;Madhamshettiwar PB;Germain RN;Smith JA;Simpson KJ;Martin SE;Buehler E;Fraser ID
RNAi筛选广泛应用于功能基因组学。虽然筛选数据可能容易受到许多实验偏差的影响，但其中许多可以通过计算分析进行校正。为此，我们开发了一个基于网络的平台，用于RNAi筛选数据的综合分析和可视化，名为CARD（用于RNAi数据的综合分析;可在https://card.niaid.nih.gov获得）。CARD允许用户在严格的数据分析工作流程中无缝执行顺序步骤，包括标准化、脱靶分析、基因表达数据整合、命中选择和网络/途径分析的最佳阈值。为了评估CARD的效用，我们描述了对三种基因组规模的siRNA筛选的分析，并证明：（i）在随后验证的命中的选择和假阳性的拒绝中的显著增加，（ii）来自相同生物学的独立筛选的命中的重叠增加，以及（iii）基于siRNA种子富集的对微小RNA（miRNA）活性的洞察。 RNAi筛选的分析是一个多步骤的过程，需要顺序使用几个不相关的资源。在这里，作者生成了一个在线资源，将RNAi分析工具和过滤器集成到一个无缝的工作流程中，从而提高了结果的特异性、选择性和再现性。
RNAi screens are widely used in functional genomics. Although the screen data can be susceptible to a number of experimental biases, many of these can be corrected by computational analysis. For this purpose, here we have developed a web-based platform for integrated analysis and visualization of RNAi screen data named CARD (for Comprehensive Analysis of RNAi Data; available at https://card.niaid.nih.gov). CARD allows the user to seamlessly carry out sequential steps in a rigorous data analysis workflow, including normalization, off-target analysis, integration of gene expression data, optimal thresholds for hit selection and network/pathway analysis. To evaluate the utility of CARD, we describe analysis of three genome-scale siRNA screens and demonstrate: (i) a significant increase both in selection of subsequently validated hits and in rejection of false positives, (ii) an increased overlap of hits from independent screens of the same biology and (iii) insight to microRNA (miRNA) activity based on siRNA seed enrichment. Analysis of RNAi screens is a multi-step process requiring the sequential use of several unrelated resources. Here the authors generate an online resource integrating RNAi analytic tools and filters into a seamless workflow, which improves the specificity, selectivity and reproducibility of the results.