Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan.
Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan.
Database (Oxford). 2019 Jan 1;2019. doi: 10.1093/database/baz075.
Integrated analysis of DNA variants and gene expression profiles may facilitate precise identification of gene regulatory networks involved in disease mechanisms. Despite the widespread availability of public resources, we lack databases that are capable of simultaneously providing gene expression profiles, variant annotations, functional prediction scores and pathogenic analyses. VariED is the first web-based querying system that integrates an annotation database and expression profiles for genetic variants. The database offers a user-friendly platform and locates gene/variant names in the literature by connecting to established online querying tools, biological annotation tools and records from free-text literature. VariED acts as a central hub for organized genome information consisting of gene annotation, variant allele frequency, functional prediction, clinical interpretation and gene expression profiles in three species: human, mouse and zebrafish. VariED also provides a novel scoring scheme to predict the functional impact of a DNA variant. With one single entry, all results regarding queried DNA variants can be downloaded. VariED can potentially serve as an efficient way to obtain comprehensive variant knowledge for clinicians and scientists around the world working on important drug discoveries and precision treatments.
整合 DNA 变异和基因表达谱的分析，可能有助于精确识别参与疾病机制的基因调控网络。尽管公共资源广泛可用，但我们缺乏能够同时提供基因表达谱、变异注释、功能预测评分和发病分析的数据库。VariED 是第一个整合注释数据库和遗传变异表达谱的基于网络的查询系统。该数据库提供了一个用户友好的平台，并通过连接到已建立的在线查询工具、生物注释工具和来自全文文献的记录，在文献中定位基因/变异名称。VariED 作为一个中央枢纽，包含了三种物种（人类、小鼠和斑马鱼）的基因注释、变异等位基因频率、功能预测、临床解释和基因表达谱的有组织的基因组信息。VariED 还提供了一种预测 DNA 变异功能影响的新评分方案。通过单一条目，可以下载与查询的 DNA 变异相关的所有结果。VariED 有可能成为一种有效的方法，为世界各地从事重要药物发现和精准治疗的临床医生和科学家提供全面的变异知识。
