RNASeqMetaDB: a database and web server for navigating metadata of publicly available mouse RNA-Seq datasets
RNASeqMetaDB: a database and web server for navigating metadata of publicly available mouse RNA-Seq datasets
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DOI：
10.1093/bioinformatics/btv503
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发表时间：
2015-12-15
期刊：
影响因子：
5.8
通讯作者：
Yu, Peng
中科院分区：
文献类型：
--
作者：
Guo, Zhengyu;Tzvetkova, Boriana;Yu, Peng
基因靶向是一种将突变引入生物体中特定基因的方案。由于体内基因功能评估和人类疾病建模的重要性，该技术已被广泛采用以产生大量的突变小鼠模型。由于最近在高通量测序技术方面的突破，RNA-Seq实验已经在许多这些小鼠模型上进行，从而产生了数百个公开可用的数据集。为了促进这些数据集的重用，我们收集了相关的元数据，并将其组织在一个名为RNASeqMetaDB的数据库中。元数据是手动管理的，以确保注释的一致性。我们开发了一个Web服务器，以方便数据库导航和数据查询。用户可以使用基因、疾病、组织类型、关键字和相关出版物等多个参数搜索数据库，以找到符合其兴趣的数据集。元数据的汇总统计数据也显示在网络服务器上，显示了RNA-Seq研究的有趣的全球模式。
Gene targeting is a protocol for introducing a mutation to a specific gene in an organism. Because of the importance of in vivo assessment of gene function and modeling of human diseases, this technique has been widely adopted to generate a large number of mutant mouse models. Due to the recent breakthroughs in high-throughput sequencing technologies, RNA-Seq experiments have been performed on many of these mouse models, leading to hundreds of publicly available datasets. To facilitate the reuse of these datasets, we collected the associated metadata and organized them in a database called RNASeqMetaDB. The metadata were manually curated to ensure annotation consistency. We developed a web server to allow easy database navigation and data querying. Users can search the database using multiple parameters like genes, diseases, tissue types, keywords and associated publications in order to find datasets that match their interests. Summary statistics of the metadata are also presented on the web server showing interesting global patterns of RNA-Seq studies.