deepBase: a database for deeply annotating and mining deep sequencing data.
deepBase: a database for deeply annotating and mining deep sequencing data.
复制标题
deepBase：用于深度注释和挖掘深度测序数据的数据库
DOI：
10.1093/nar/gkp943
复制
发表时间：
2010-01
影响因子：
14.9
通讯作者：
Qu LH
中科院分区：
文献类型：
--
作者：
Yang JH;Shao P;Zhou H;Chen YQ;Qu LH
高通量下一代测序技术的进步重塑了转录组学研究的格局。然而，对这些海量数据的探索仍然是一项艰巨的挑战。在这项研究中，我们描述了一个新的数据库，deepBase，我们开发了它来促进从转录组学数据中全面注释和发现小rna。目前发布的deepBase包含来自7种生物不同组织和细胞系的185个小RNA文库的深度测序数据：人类、小鼠、鸡、鸡肠、黑腹果蝇、秀丽隐门线虫和拟南芥。通过分析完美映射到超过2.84亿个基因组位点的~ 1460万个独特reads，我们注释并鉴定了~ 38万个独特的ncrna相关小rna (nasrna)， ~ 150万个独特的启动子相关小rna (pasrna)， ~ 400万个独特的外显子相关小rna （easrna）和~ 600万个独特的重复子相关小rna （rasrna）。此外，miRDeep和snoSeeker预测了2038个miRNA和1889个snoRNA候选物。所有被映射的读段可以被分成大约120万个RNA簇。为了比较分析的目的，deepBase提供了一个综合的、交互的和多功能的显示。网站亦提供方便的搜寻选项、相关刊物及其他有用资料，以供进一步调查。deepBase的网址是：http://deepbase.sysu.edu.cn/。
Advances in high-throughput next-generation sequencing technology have reshaped the transcriptomic research landscape. However, exploration of these massive data remains a daunting challenge. In this study, we describe a novel database, deepBase, which we have developed to facilitate the comprehensive annotation and discovery of small RNAs from transcriptomic data. The current release of deepBase contains deep sequencing data from 185 small RNA libraries from diverse tissues and cell lines of seven organisms: human, mouse, chicken, Ciona intestinalis, Drosophila melanogaster, Caenhorhabditis elegans and Arabidopsis thaliana. By analyzing ∼14.6 million unique reads that perfectly mapped to more than 284 million genomic loci, we annotated and identified ∼380 000 unique ncRNA-associated small RNAs (nasRNAs), ∼1.5 million unique promoter-associated small RNAs (pasRNAs), ∼4.0 million unique exon-associated small RNAs (easRNAs) and ∼6 million unique repeat-associated small RNAs (rasRNAs). Furthermore, 2038 miRNA and 1889 snoRNA candidates were predicted by miRDeep and snoSeeker. All of the mapped reads can be grouped into about 1.2 million RNA clusters. For the purpose of comparative analysis, deepBase provides an integrative, interactive and versatile display. A convenient search option, related publications and other useful information are also provided for further investigation. deepBase is available at: http://deepbase.sysu.edu.cn/.
登录
查看更多内容
影响因子：
56.9
作者：
Kapranov, Philipp;Cheng, Jill;Gingeras, Thomas R.
通讯作者：
Gingeras, Thomas R.
影响因子：
10.5
作者：
Babiarz, Joshua E.;Ruby, J. Graham;Blelloch, Robert
通讯作者：
Blelloch, Robert
Mirbase：MicroRNA基因组学的工具。
影响因子：
14.9
作者：
Griffiths-Jones, Sam;Saini, Harpreet Kaur;van Dongen, Stijn;Enright, Anton J.
通讯作者：
Enright, Anton J.
影响因子：
16.8
作者：
Gabel, Harrison W.;Ruvkun, Gary
通讯作者：
Ruvkun, Gary
影响因子：
30.8
作者：
Faulkner, Geoffrey J.;Kimura, Yasumasa;Carninci, Piero
通讯作者：
Carninci, Piero