（工具篇）S4E26:环状RNA常用数据库介绍总结
现在很多朋友都在关注环状RNA(circular RNA)，不过与lncRNA和microRNA相比，环状RNA数据库还是相对比较少的，我们今天就总结和简单介绍一下。
1. circBase
网址：http://www.circbase.org/
Thousands of circular RNAs (circRNAs) have recently been shown to be expressed in eukaryotic cells [, , , ]. Here you can explore public circRNA datasets and download the custom python scripts needed to discover circRNAs in your own (ribominus) RNA-seq data.
数据库功能：
Sequence-based search
Search the database by identifier, gene description, genomic position, or their lists.
Retrieve dataset slices by defining a set of conditions (table browser).
Export tables in a variety of formats.
Export FASTA files containing genomic sequence.
比如我们想查询FoxO3相关的环状RNA，可以直接在搜索框输入FoxO3，结果如下：
可以看到人的两条和小鼠中的三条circRNA，并可进一步点开查看。
2. CircNet：a database of circular RNAs derived from transcriptome sequencing data
网址：http://circnet.mbc.nctu.edu.tw/
基于转录组测序的数据建立的数据库，收录以下信息:
novel circRNAs,
integrated miRNA-target networks,
expression profiles of circRNA isoforms,
genomic annotations of circRNA isoforms (e.g. 282 948 exon positions), and
sequences of circRNA isoforms.
比如我们想查询FoxO3相关的环状RNA，可以直接在搜索框输入FoxO3，结果如下：
如图所示，不仅显示了FoxO3相关的环状RNA circ-FOXO3.1，还显示了microRNA，右侧上面显示 circ-FOXO3.1在染色体上的位置，右侧下面可以根据位置对 circ-FOXO3.1进行查询显示，右侧上面点击Expression表达显示在不同组织中的表达水平：
3. deepbase：a platform for annotating and discovering small and long ncRNAs (microRNAs, siRNAs, piRNAs...) from next generation sequencing data.
网址：http://deepbase.sysu.edu.cn/
这个数据库的的功能：
deepView Genome Browser: visualization map
microRNAs and other ncRNAs expression pattern
predicted RNA clusters
predicted microRNAs
predicted snoRNAs
browse microRNAs and ncRNA-associated small RNAs
nasView Browser: comparisons of multiple libraries for ncRNAs
browse promoter-associated and exon-associated small RNAs
browse repeat-associated small RNAs
libView Browser: comparisons of multiple libraries
common search or Search homologous reads
包括的信息比较全，功能强大，除了circRNA外，lncRNA等信息也有，既可以浏览，也可以搜索。如果要搜索circRNA，可以直接打开网址:
http://biocenter.sysu.edu.cn/deepBase/browse_circRNA.php?SClade=mammal&SOrganism=hg19&Choose=Choose
同样可以检索到一条foxO3的相关信息。
4. Starbase：收录包括microRNA、mRNA、lncRNA等多种分子的信息
如果检索与circRNA有关的，可打开circRNABase: miRNA-circRNA interaction Descriptions，网址：http://starbase.sysu.edu.cn/mirCircRNA.php，输入microRNA或者circRNA检索，比如检索microRNA125有关的circRNA：
结果：
下面两个是没有检索成功的两个数据库，大家可以尝试下。
5.CircInteractome：
网址：http://circinteractome.nia.nih.gov/
Hundreds of RNA-binding proteins and miRNAs has been shown to regulate gene expression in mammals. Recently, circular RNAs (circRNAs) have been reported to regulate gene expression by sponging miRNA. Here we have used 109 datasets of RNA-binding proteins (RBPs) and queried circRNAs (Glažar et al. 2014) for RNA-binding sites. CircInteractome predicts the miRNAs which can potentially target the circRNAs using the Targetscan prediction tool (Grimson et al., 2007). This computational tool enables the prediction and mapping of binding sites for RBPs and miRNAs on reported circRNAs.
预测能够结合circRNA的蛋白和microRNA
功能包括：
Searches circRNAs name
Searches the genomic position and best-matching transcripts of the circRNA
Retrieves genomic and mature circRNA sequences
Searches RBPs binding to a circRNA and to sequences upstream/downstream of the circRNA
Identifies RBPs binding to the circRNA junctions
Identifies miRNAs targeting a circRNA
Designs divergent primers for circRNAs
Designs siRNAs Specific to circRNA
6. Circ2Traits：a comprehensive database for circular RNA potentially associated with disease and traits. 网址：http://gyanxet-beta.com/circdb/
That’s all. Thank you!
请关注“小张聊科研”：搜索微信号“xzlky2015”，或长按二维码识别关注。
↓↓↓