Automated Isoform Diversity Detector (AIDD): a pipeline for investigating transcriptome diversity of RNA-seq data.
Automated Isoform Diversity Detector (AIDD): a pipeline for investigating transcriptome diversity of RNA-seq data.
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DOI：
10.1186/s12859-020-03888-6
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发表时间：
2020-12-30
影响因子：
3
通讯作者：
Piontkivska H
中科院分区：
文献类型：
--
作者：
Plonski NM;Johnson E;Frederick M;Mercer H;Fraizer G;Meindl R;Casadesus G;Piontkivska H
随着可用于探索转录组多样性的RNA-seq数据集的数量增加，对易于使用的综合计算工作流程的需求也在增加。许多可用的工具有助于分析转录组多样性的两种主要机制之一，即由于选择性剪接而导致的异构体的差异表达，而第二种主要机制-由于单个核苷酸转录后的变化导致的RNA编辑-仍然被忽视。这两种机制在生理和疾病过程中都起着至关重要的作用，包括癌症和神经疾病。然而，在转录组水平上阐明RNA编辑事件需要越来越复杂的计算工具，这反过来又导致对大规模高通量变体调用应用感兴趣但缺乏人力和/或计算专业知识的实验室面临巨大的准入障碍。在这里，我们提出了一个易于使用的、全自动化的计算管道(自动异形多样性检测器，AIDD)，它包含用于绘制转录组多样性图所需的各种任务的开源工具，包括RNA编辑事件。为了便于重现性和避免系统依赖，管道包含在预配置的VirtualBox环境中。分析任务和格式转换是通过一组自动脚本完成的，这些脚本使用户能够在一个步骤中从一组原始数据(如FASTQ文件)转换为可供发布的结果和数字。一个可公开获得的寨卡病毒感染的神经前体细胞数据集被用来说明艾滋病的能力。AIDD管道为全面和可重复的RNA-SEQ分析提供了一个用户友好的界面。在AIDD的独特功能中，它能够推断RNA编辑模式，包括ADAR编辑，并包括用于此类编辑景观的时间序列分析的Guttman标度模式。基于AIDD的结果表明ADAR亚型的多样性、与先天性免疫系统和病毒感染有关的关键RNA编辑酶的重要性。这些发现为ADAR编辑失调在包括先天性寨卡综合征在内的疾病机制中的潜在作用提供了见解。由于其自动化的包罗万象的功能，AIDD管道使即使是新手用户也能够轻松地探索转录组多样性的常见机制，包括RNA编辑景观。
As the number of RNA-seq datasets that become available to explore transcriptome diversity increases, so does the need for easy-to-use comprehensive computational workflows. Many available tools facilitate analyses of one of the two major mechanisms of transcriptome diversity, namely, differential expression of isoforms due to alternative splicing, while the second major mechanism—RNA editing due to post-transcriptional changes of individual nucleotides—remains under-appreciated. Both these mechanisms play an essential role in physiological and diseases processes, including cancer and neurological disorders. However, elucidation of RNA editing events at transcriptome-wide level requires increasingly complex computational tools, in turn resulting in a steep entrance barrier for labs who are interested in high-throughput variant calling applications on a large scale but lack the manpower and/or computational expertise. Here we present an easy-to-use, fully automated, computational pipeline (Automated Isoform Diversity Detector, AIDD) that contains open source tools for various tasks needed to map transcriptome diversity, including RNA editing events. To facilitate reproducibility and avoid system dependencies, the pipeline is contained within a pre-configured VirtualBox environment. The analytical tasks and format conversions are accomplished via a set of automated scripts that enable the user to go from a set of raw data, such as fastq files, to publication-ready results and figures in one step. A publicly available dataset of Zika virus-infected neural progenitor cells is used to illustrate AIDD’s capabilities. AIDD pipeline offers a user-friendly interface for comprehensive and reproducible RNA-seq analyses. Among unique features of AIDD are its ability to infer RNA editing patterns, including ADAR editing, and inclusion of Guttman scale patterns for time series analysis of such editing landscapes. AIDD-based results show importance of diversity of ADAR isoforms, key RNA editing enzymes linked with the innate immune system and viral infections. These findings offer insights into the potential role of ADAR editing dysregulation in the disease mechanisms, including those of congenital Zika syndrome. Because of its automated all-inclusive features, AIDD pipeline enables even a novice user to easily explore common mechanisms of transcriptome diversity, including RNA editing landscapes.
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