LncATLAS database for subcellular localization of long noncoding RNAs
LncATLAS database for subcellular localization of long noncoding RNAs
复制标题
DOI：
10.1261/rna.060814.117
复制
发表时间：
2017-07-01
期刊：
影响因子：
4.5
通讯作者：
Johnson, Rory
中科院分区：
文献类型：
--
作者：
Mas-Ponte, David;Carlevaro-Fita, Joana;Johnson, Rory
长链非编码RNA（IncRNA）的亚细胞定位为研究其分子功能提供了有价值的线索。然而，测量新发现的IncRNA的定位涉及耗时且昂贵的实验方法。我们已经创建了“IncATLAS”，这是一个基于RNA测序数据集的人类细胞中IncRNA定位的综合资源。总共有6768个GENCODE注释的IncRNA在15个细胞系的各个区室中呈现。我们引入相对浓度指数（RCI）作为来自系综RNA-seq测量的定位的有用量度。lncATLAS可通过直观且信息丰富的网络服务器访问，从中使用标识符或名称访问感兴趣的IncRNA。定位在细胞类型和细胞器中呈现，并且可以与所有其他基因的分布进行比较。每次查询都会自动生成出版质量的数字和原始数据表，整个数据集也可供下载。LncATLAS使IncRNA亚细胞定位数据可供尽可能多的研究人员使用。它可在Incatlas.crg.eu获得。
The subcellular localization of long noncoding RNAs (IncRNAs) holds valuable clues to their molecular function. However, measuring localization of newly discovered IncRNAs involves time-consuming and costly experimental methods. We have created "IncATLAS," a comprehensive resource of IncRNA localization in human cells based on RNA-sequencing data sets. Altogether, 6768 GENCODE-annotated IncRNAs are represented across various compartments of 15 cell lines. We introduce relative concentration index (RCI) as a useful measure of localization derived from ensemble RNA-seq measurements. LncATLAS is accessible through an intuitive and informative webserver, from which IncRNAs of interest are accessed using identifiers or names. Localization is presented across cell types and organelles, and may be compared to the distribution of all other genes. Publication-quality figures and raw data tables are automatically generated with each query, and the entire data set is also available to download. LncATLAS makes IncRNA subcellular localization data available to the widest possible number of researchers. It is available at Incatlas.crg.eu.