omiRas：一个 Web 服务器，用于分析从小 RNA-Seq 数据中衍生的 miRNAs 的差异表达。

omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data.

机构信息

Plant Molecular Biology, Institute of Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Str.9, 60439 Frankfurt am Main, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, 60438 Frankfurt am Main and Molecular Bioinformatics Group, Institute of Computer Science, Faculty of Computer Science and Mathematics, Cluster of Excellence, Frankfurt "Macromolecular Complexes", Robert-Mayer-Strasse 11-15, 60325 Frankfurt am Main, Germany.

出版信息

Bioinformatics. 2013 Oct 15;29(20):2651-2. doi: 10.1093/bioinformatics/btt457. Epub 2013 Aug 13.

DOI:10.1093/bioinformatics/btt457

PMID:23946503

Abstract

SUMMARY

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.

AVAILABILITY AND IMPLEMENTATION

The omiRas Web server is implemented in Python, PostgreSQL, R and can be accessed at: http://tools.genxpro.net/omiras/.

摘要

小 RNA 深度测序被广泛用于描述两种状态（例如健康和患病个体）之间差异表达的非编码 RNA（ncRNA），并深入了解特定于状态的表型特征的分子机制。ncRNA 组由多种 RNA 组成，例如转移 RNA、小核仁 RNA 和 microRNA（miRNA）等。在这里，我们介绍了 omiRas，这是一个用于注释、比较和可视化来自两种不同条件的下一代测序实验的 ncRNA 相互作用网络的 Web 服务器。该 Web 工具允许用户提交原始测序数据，结果以以下形式呈现：（i）静态注释结果，包括每个文库的长度分布、映射统计信息、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 相互作用数据库的组合，选择 miRNA 和其靶基因的交互式网络可视化。