miRNet 2.0: network-based visual analytics for miRNA functional analysis and systems biology
miRNet 2.0: network-based visual analytics for miRNA functional analysis and systems biology
复制标题
DOI：
10.1093/nar/gkaa467
复制
发表时间：
2020-07-02
影响因子：
14.9
通讯作者：
Xia, Jianguo
中科院分区：
文献类型：
--
作者：
Chang, Le;Zhou, Guangyan;Xia, Jianguo
MiRNet是一个易于使用的基于网络的平台，旨在通过基于网络的可视分析将用户数据与现有知识相结合，帮助阐明microRNA(MiRNA)的功能。自2016年首次发布以来，全球已有2万名研究人员访问了miRNet，每天有近100名用户。虽然版本1.0主要侧重于miRNA与靶基因的相互作用，但很明显，为了获得对miRNA功能的全局看法，有必要在分析过程中将其他重要参与者纳入其中。在这一概念的驱动下，在miRNet 2.0版中，我们(I)增加了对影响miRNAs、miRNA结合位点或靶基因的转录因子(TF)和单核苷酸多态(SNPs)的支持，同时还极大地(5倍地)增加了miRNAs、ncRNAs和疾病关联的基础知识库；(Ii)实现了新功能，允许创建和可视化探索多方网络，增强了对原位功能分析的支持；(Iii)改进了Web界面，优化了工作流程，并引入了微服务和Web应用程序编程接口(API)，以保持高性能的实时数据分析。底层的R包也与2.0版一起发布，以便为R程序员提供更灵活的数据分析。MiRNet2.0网站可在https://www.mirnet.ca.免费获得
miRNet is an easy-to-use, web-based platform designed to help elucidate microRNA (miRNA) functions by integrating users' data with existing knowledge via network-based visual analytics. Since its first release in 2016, miRNet has been accessed by >20 000 researchers worldwide, with similar to 100 users on a daily basis. While version 1.0 was focused primarily on miRNA-target gene interactions, it has become clear that in order to obtain a global view of miRNA functions, it is necessary to bring other important players into the context during analysis. Driven by this concept, in miRNet version 2.0, we have (i) added support for transcription factors (TFs) and single nucleotide polymorphisms (SNPs) that affect miRNAs, miRNA-binding sites or target genes, whilst also greatly increased (>5-fold) the underlying knowledgebases of miRNAs, ncRNAs and disease associations; (ii) implemented new functions to allow creation and visual exploration of multipartite networks, with enhanced support for in situ functional analysis and (iii) revamped the web interface, optimized the workflow, and introduced microservices and web application programming interface (API) to sustain high-performance, real-time data analysis. The underlying R package is also released in tandem with version 2.0 to allow more flexible data analysis for R programmers. The miRNet 2.0 website is freely available at https://www.mirnet.ca.