The Molecular Subtyping Resource (MouSR): a user-friendly tool for rapid biological discovery from human or mouse transcriptional data
The Molecular Subtyping Resource (MouSR): a user-friendly tool for rapid biological discovery from human or mouse transcriptional data
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DOI：
10.1101/2021.08.12.456127
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发表时间：
2021-08
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通讯作者：
Baharak Ahmaderaghi;R. Amirkhah;J. Jackson;T. Lannagan;K. Gilroy;Sudhir B Malla;K. Redmond;Timothy S. Maughan;S. Leedham;Andrew Campbell;O. Sansom;M. Lawler;P. Dunne
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文献类型：
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作者：
Baharak Ahmaderaghi;R. Amirkhah;J. Jackson;T. Lannagan;K. Gilroy;Sudhir B Malla;K. Redmond;Timothy S. Maughan;S. Leedham;Andrew Campbell;O. Sansom;M. Lawler;P. Dunne
在过去的十年中，转录数据的生成急剧增加，推动了分析算法的发展，使分析样本的生物学基础成为可能。然而，这些资源要求用户具有数据整理和分析方面的专业知识，减少了“湿实验室”用户使用有限的编程技能进行生物发现的机会。尽管存在商业解决方案，但软件访问的成本可能使学术研究团体望而却步。为了应对这些挑战，我们开发了一个开源和用户友好的数据分析平台，用于对来自人类或小鼠组织的转录数据进行实时生物信息学询问，称为“MouSR”。这个可访问互联网的分析工具https://mousr.qub.ac.uk/使用户能够使用直观的“点按”界面轻松查询他们的数据，其中包括一套分子表征选项，包括QC，差异基因表达，基因集富集和RNA-Seq的微环境细胞群分析。为用户提供了分析参数的可调选项，以生成可以保存为出版质量图像的结果。为了突出其执行高质量数据分析的能力，我们利用MouSR工具查询我们最近发表的肿瘤数据集，这些数据集来自基因工程小鼠模型和匹配的类器官，在那里我们快速重现了关键的转录发现。MouSR在线工具为用户提供了一个独特的免费选项，可以对支持转录数据集的信号进行快速转录组学分析和全面查询，从而缓解了生物学发现的主要瓶颈。
Generation of transcriptional data has dramatically increased in the last decade, driving the development of analytical algorithms that enable interrogation of the biology underpinning the profiled samples. However, these resources require users to have expertise in data wrangling and analytics, reducing opportunities for biological discovery by “wet-lab” users with a limited programming skillset. Although commercial solutions exist, costs for software access can be prohibitive for academic research groups. To address these challenges, we have developed an open source and user-friendly data analysis platform for on-the-fly bioinformatic interrogation of transcriptional data derived from human or mouse tissue, called “MouSR”. This internet-accessible analytical tool, https://mousr.qub.ac.uk/, enables users to easily interrogate their data using an intuitive “point and click” interface, which includes a suite of molecular characterisation options including QC, differential gene expression, gene set enrichment and microenvironmental cell population analyses from RNA-Seq. Users are provided with adjustable options for analysis parameters to generate results that can be saved as publication-quality images. To highlight its ability to perform high quality data analysis, we utilise the MouSR tool to interrogate our recently published tumour dataset, derived from genetically engineered mouse models and matched organoids, where we rapidly reproduced the key transcriptional findings. The MouSR online tool provides a unique freely-available option for users to perform rapid transcriptomic analyses and comprehensive interrogation of the signalling underpinning transcriptional datasets, which alleviates a major bottleneck for biological discovery.