Hinske Ludwig Christian, França Gustavo S, Torres Hugo A M, Ohara Daniel T, Lopes-Ramos Camila M, Heyn Jens, Reis Luiz F L, Ohno-Machado Lucila, Kreth Simone, Galante Pedro A F
Clinic of Anaesthesiology, Clinic of the University of Munich, Munich, Germany
Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
Database (Oxford). 2014 Oct 6;2014. doi: 10.1093/database/bau099. Print 2014.
MicroRNAs (miRNAs) are a class of small (∼22 nucleotides) non-coding RNAs that post-transcriptionally regulate gene expression by interacting with target mRNAs. A majority of miRNAs is located within intronic or exonic regions of protein-coding genes (host genes), and increasing evidence suggests a functional relationship between these miRNAs and their host genes. Here, we introduce miRIAD, a web-service to facilitate the analysis of genomic and structural features of intragenic miRNAs and their host genes for five species (human, rhesus monkey, mouse, chicken and opossum). miRIAD contains the genomic classification of all miRNAs (inter- and intragenic), as well as classification of all protein-coding genes into host or non-host genes (depending on whether they contain an intragenic miRNA or not). We collected and processed public data from several sources to provide a clear visualization of relevant knowledge related to intragenic miRNAs, such as host gene function, genomic context, names of and references to intragenic miRNAs, miRNA binding sites, clusters of intragenic miRNAs, miRNA and host gene expression across different tissues and expression correlation for intragenic miRNAs and their host genes. Protein-protein interaction data are also presented for functional network analysis of host genes. In summary, miRIAD was designed to help the research community to explore, in a user-friendly environment, intragenic miRNAs, their host genes and functional annotations with minimal effort, facilitating hypothesis generation and in-silico validations. Database URL: http://www.miriad-database.org.
微小RNA（miRNA）是一类小的（约22个核苷酸）非编码RNA，通过与靶mRNA相互作用在转录后调节基因表达。大多数miRNA位于蛋白质编码基因（宿主基因）的内含子或外显子区域内，越来越多的证据表明这些miRNA与其宿主基因之间存在功能关系。在这里，我们介绍了miRIAD，这是一个网络服务，用于促进对人类、恒河猴、小鼠、鸡和负鼠这五个物种的基因内miRNA及其宿主基因的基因组和结构特征进行分析。miRIAD包含所有miRNA（基因间和基因内）的基因组分类，以及所有蛋白质编码基因分为宿主或非宿主基因的分类（取决于它们是否包含基因内miRNA）。我们从多个来源收集和处理了公共数据，以清晰地可视化与基因内miRNA相关的知识，如宿主基因功能、基因组背景、基因内miRNA的名称和参考文献、miRNA结合位点、基因内miRNA簇、不同组织中miRNA和宿主基因的表达以及基因内miRNA与其宿主基因的表达相关性。还提供了蛋白质-蛋白质相互作用数据用于宿主基因的功能网络分析。总之，miRIAD旨在帮助研究界在用户友好的环境中轻松探索基因内miRNA、其宿主基因和功能注释，促进假设生成和计算机模拟验证。数据库网址：http://www.miriad-database.org。
