miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression.
miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression.
复制标题
DOI：
10.1186/1471-2105-10-328
复制
发表时间：
2009-10-12
影响因子：
3
通讯作者：
Lin NS
中科院分区：
文献类型：
--
作者：
Wang WC;Lin FM;Chang WC;Lin KY;Huang HD;Lin NS
微小RNA（miRNA）是一种长度为19至25 nt的小型非编码RNA，在动物和植物的基因调控中发挥着重要作用。近年来，寡核苷酸芯片技术成为检测miRNA表达的一种高通量、稳健的方法。然而，该方法仅限于检测已知miRNA的表达。第二代测序是一种廉价且高通量的测序方法。这种新方法是一种有前途的工具，具有高灵敏度和特异性，可用于测量样品中小RNA序列的丰度。因此，miRNA的表达谱可以涉及使用测序而不是寡核苷酸阵列。此外，该方法还可用于发现新的miRNAs。这项工作提出了一种系统的方法，miRExpress，用于从第二代测序技术获得的测序读数中提取miRNA表达谱。实现了一个独立的软件包，用于从RNA的高通量测序生成miRNA表达谱，而不需要测序的基因组。该软件也是一个数据库支持的，高效和灵活的工具，用于研究miRNA调控。此外，我们证明了利用miRExpress从两个Illumina数据集构建的人类和植物物种中提取miRNA表达谱。我们开发了miRExpress，这是一个数据库支持的，高效和灵活的工具，用于检测miRNA表达谱。通过对两个Illumina数据集的分析，验证了miRExpress在获取miRNA表达谱方面的有效性，并显示了其在寻找新的miRNA方面的可用性。
MicroRNAs (miRNAs), small non-coding RNAs of 19 to 25 nt, play important roles in gene regulation in both animals and plants. In the last few years, the oligonucleotide microarray is one high-throughput and robust method for detecting miRNA expression. However, the approach is restricted to detecting the expression of known miRNAs. Second-generation sequencing is an inexpensive and high-throughput sequencing method. This new method is a promising tool with high sensitivity and specificity and can be used to measure the abundance of small-RNA sequences in a sample. Hence, the expression profiling of miRNAs can involve use of sequencing rather than an oligonucleotide array. Additionally, this method can be adopted to discover novel miRNAs. This work presents a systematic approach, miRExpress, for extracting miRNA expression profiles from sequencing reads obtained by second-generation sequencing technology. A stand-alone software package is implemented for generating miRNA expression profiles from high-throughput sequencing of RNA without the need for sequenced genomes. The software is also a database-supported, efficient and flexible tool for investigating miRNA regulation. Moreover, we demonstrate the utility of miRExpress in extracting miRNA expression profiles from two Illumina data sets constructed for the human and a plant species. We develop miRExpress, which is a database-supported, efficient and flexible tool for detecting miRNA expression profile. The analysis of two Illumina data sets constructed from human and plant demonstrate the effectiveness of miRExpress to obtain miRNA expression profiles and show the usability in finding novel miRNAs.
登录
查看更多内容
影响因子：
3.7
作者：
Fahlgren N;Howell MD;Kasschau KD;Chapman EJ;Sullivan CM;Cumbie JS;Givan SA;Law TF;Grant SR;Dangl JL;Carrington JC
通讯作者：
Carrington JC
影响因子：
4
作者：
Das, Asis K.;Carmichael, Gordon G.
通讯作者：
Carmichael, Gordon G.
影响因子：
7
作者：
Reid, Jeffrey G.;Nagaraja, Ankur K.;Gunaratne, Preethi H.
通讯作者：
Gunaratne, Preethi H.
影响因子：
7
作者：
Morin, Ryan D.;O'Connor, Michael D.;Marra, Marco A.
通讯作者：
Marra, Marco A.
影响因子：
3
作者：
Smith AD;Xuan Z;Zhang MQ
通讯作者：
Zhang MQ