FIVEx：跨公共数据集的交互式 eQTL 浏览器。
FIVEx: an interactive eQTL browser across public datasets.
机构信息
Department of Biostatistics, The Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA.
出版信息
Bioinformatics. 2022 Jan 3;38(2):559-561. doi: 10.1093/bioinformatics/btab614.
SUMMARY
Expression quantitative trait loci (eQTLs) characterize the associations between genetic variation and gene expression to provide insights into tissue-specific gene regulation. Interactive visualization of tissue-specific eQTLs or splice QTLs (sQTLs) can facilitate our understanding of functional variants relevant to disease-related traits. However, combining the multi-dimensional nature of eQTLs/sQTLs into a concise and informative visualization is challenging. Existing QTL visualization tools provide useful ways to summarize the unprecedented scale of transcriptomic data but are not necessarily tailored to answer questions about the functional interpretations of trait-associated variants or other variants of interest. We developed FIVEx, an interactive eQTL/sQTL browser with an intuitive interface tailored to the functional interpretation of associated variants. It features the ability to navigate seamlessly between different data views while providing relevant tissue- and locus-specific information to offer users a better understanding of population-scale multi-tissue transcriptomic profiles. Our implementation of the FIVEx browser on the EBI eQTL catalogue, encompassing 16 publicly available RNA-seq studies, provides important insights for understanding potential tissue-specific regulatory mechanisms underlying trait-associated signals.
AVAILABILITY AND IMPLEMENTATION
A FIVEx instance visualizing EBI eQTL catalogue data can be found at https://fivex.sph.umich.edu. Its source code is open source under an MIT license at https://github.com/statgen/fivex.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
表达数量性状基因座（eQTLs）描述了遗传变异与基因表达之间的关联，为理解组织特异性基因调控提供了线索。组织特异性 eQTL 或剪接 QTL（sQTL）的交互式可视化可以帮助我们理解与疾病相关性状相关的功能变体。然而，将 eQTL/sQTL 的多维性质组合成简洁且信息丰富的可视化是具有挑战性的。现有的 QTL 可视化工具为总结转录组数据的空前规模提供了有用的方法，但不一定针对与性状相关变体或其他感兴趣变体的功能解释问题进行了优化。我们开发了 FIVEx，这是一种具有直观界面的交互式 eQTL/sQTL 浏览器，专门针对相关变体的功能解释进行了优化。它具有在不同数据视图之间无缝导航的功能，同时提供相关的组织和基因座特异性信息，使用户更好地理解群体规模的多组织转录组谱。我们在 EBI eQTL 目录上实现了 FIVEx 浏览器，该目录包含 16 个公开的 RNA-seq 研究，为理解与性状相关信号相关的潜在组织特异性调节机制提供了重要的见解。
可用性和实现
可以在 https://fivex.sph.umich.edu 上找到可视化 EBI eQTL 目录数据的 FIVEx 实例。其源代码在 MIT 许可证下以开源形式在 https://github.com/statgen/fivex 上提供。
补充信息
补充数据可在生物信息学在线获得。
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