Glogovitis Ilias, Yahubyan Galina, Würdinger Thomas, Koppers-Lalic Danijela, Baev Vesselin
Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria.
Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.
Cancers (Basel). 2021 Nov 12;13(22):5663. doi: 10.3390/cancers13225663.
Tools for microRNA (miR) sequencing data analyses are broadly used in biomedical research. However, the complexity of computational approaches still remains a challenge for biologists with scarce experience in data analytics and bioinformatics. Here, we present miRGalaxy, a Galaxy-based framework for comprehensive analysis of miRs and their sequence variants-miR isoforms (isomiRs). Though isomiRs are commonly reported in deep-sequencing experiments, their detailed structure complexity and specific differential expression (DE) remain not fully examined by the majority of the available analysis tools. miRGalaxy encompasses biologist-user-friendly tools and workflows dedicated to the analysis of the isomiR-ome and its complex behavior in various biological samples. miRGalaxy is developed as a modular, accessible, redistributable, shareable, and user-friendly framework for scientists working with small RNA (sRNA)-seq data. Due to its modular workflow, advanced users can customize the steps and tools for their needs. In addition, the framework provides an analysis report where the significant output results are summarized in charts and visualizations. miRGalaxy can be accessed via preconfigured Docker image flavor and a Toolshed installation if the user already has a running Galaxy instance. Over the last decade, studies on the expression of miRs and isomiRs in normal and deregulated tissues have led to the discovery of their potential as diagnostic biomarkers. The detection of miRs in biofluids further expanded the exploration of the miR repertoire as a source of liquid biopsy biomarkers. Here we show the miRGalaxy framework application for in-depth analysis of the sRNA-seq data from two different biofluids, milk and plasma, to identify, annotate, and discover specific differentially expressed miRs and isomiRs.
微小RNA（miR）测序数据分析工具在生物医学研究中广泛应用。然而，对于缺乏数据分析和生物信息学经验的生物学家而言，计算方法的复杂性仍是一项挑战。在此，我们展示了miRGalaxy，这是一个基于Galaxy的框架，用于全面分析miR及其序列变体——miR异构体（isomiRs）。尽管在深度测序实验中常报道有isomiRs，但大多数现有分析工具仍未充分研究其详细的结构复杂性和特定的差异表达（DE）。miRGalaxy包含便于生物学家使用的工具和工作流程，专门用于分析isomiR组及其在各种生物样本中的复杂行为。miRGalaxy是为处理小RNA（sRNA）测序数据的科学家开发的一个模块化、可访问、可重新分发、可共享且用户友好的框架。由于其模块化工作流程，高级用户可以根据自身需求定制步骤和工具。此外，该框架还提供一份分析报告，其中重要的输出结果以图表和可视化形式进行总结。如果用户已有运行的Galaxy实例，可通过预配置的Docker镜像风格和工具库安装来访问miRGalaxy。在过去十年中，对正常组织和失调组织中miR和isomiR表达的研究已发现它们作为诊断生物标志物的潜力。生物流体中miR的检测进一步扩展了对miR库作为液体活检生物标志物来源的探索。在此，我们展示了miRGalaxy框架在深入分析来自两种不同生物流体（牛奶和血浆）的sRNA测序数据方面的应用，以识别、注释和发现特定的差异表达miR和isomiR。
