omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data
omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data
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DOI：
10.1093/bioinformatics/btt457
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发表时间：
2013-10-15
期刊：
影响因子：
5.8
通讯作者：
Rotter, Bjoern
中科院分区：
文献类型：
--
作者：
Mueller, Soeren;Rycak, Lukas;Rotter, Bjoern
小RNA深度测序被广泛用于表征两种条件之间差异表达的非编码RNA（ncRNA），例如。G.健康和患病个体，并揭示条件特异性表型性状的分子机制的见解。ncRNAome是由大量的RNA组成，如转移RNA，小核仁RNA和microRNA（miRNA），仅举几例。在这里，我们提出omiRas，一个Web服务器的注释，比较和可视化的相互作用网络的ncRNA来自下一代测序实验的两种不同的条件。Web工具允许用户提交原始测序数据，结果显示为：（i）静态注释结果，包括每个文库的长度分布、映射统计、比对和定量表以及条件之间差异表达的ncRNA列表，以及（ii）基于几个miRNA-mRNA相互作用数据库组合的用户选择的miRNA及其靶基因的交互式网络可视化。
Small RNA deep sequencing is widely used to characterize non-coding RNAs (ncRNAs) differentially expressed between two conditions, e. g. healthy and diseased individuals and to reveal insights into molecular mechanisms underlying condition-specific phenotypic traits. The ncRNAome is composed of a multitude of RNAs, such as transfer RNA, small nucleolar RNA and microRNA (miRNA), to name few. Here we present omiRas, a Web server for the annotation, comparison and visualization of interaction networks of ncRNAs derived from next-generation sequencing experiments of two different conditions. The Web tool allows the user to submit raw sequencing data and results are presented as: (i) static annotation results including length distribution, mapping statistics, alignments and quantification tables for each library as well as lists of differentially expressed ncRNAs between conditions and (ii) an interactive network visualization of user-selected miRNAs and their target genes based on the combination of several miRNA-mRNA interaction databases.