MiRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting.
MiRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting.
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DOI：
10.1093/nar/gks1168
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发表时间：
2013-01
影响因子：
14.9
通讯作者：
Lee S
中科院分区：
文献类型：
--
作者：
Cho S;Jang I;Jun Y;Yoon S;Ko M;Kwon Y;Choi I;Chang H;Ryu D;Lee B;Kim VN;Kim W;Lee S
生物发生和分子功能是microRNA （miRNA）研究领域的两个重点课题。深度测序已成为编目miRNA曲目和产生表达谱以公正的方式的主要技术。在这里，我们描述了miRGator v3.0更新（http://mirgator.kobic.re.kr），它编译了公开的深度测序miRNA数据，并实现了几个新的工具来促进对大量数据的探索。miR-seq浏览器支持用户检查与二级结构的短读对齐以及并发窗口中可用的读计数信息。序列编辑、排序、排序、用户数据的导入和导出等功能将对研究iso-miRs、miRNA编辑和修改有很大的帮助。miRNA - target关系是理解miRNA功能的基础。基于来自同一样本的miRNA-seq和RNA-seq数据，miRNA和靶mrna的共表达分析在热图和网络视图中可视化，用户可以研究基因表达和靶关系的负相关，这些数据来自各种预测和验证的靶标数据库。通过保持最新的数据集和分析工具，miRGator应该继续作为mirna生物发生和功能研究的综合资源。
Biogenesis and molecular function are two key subjects in the field of microRNA (miRNA) research. Deep sequencing has become the principal technique in cataloging of miRNA repertoire and generating expression profiles in an unbiased manner. Here, we describe the miRGator v3.0 update (http://mirgator.kobic.re.kr) that compiled the deep sequencing miRNA data available in public and implemented several novel tools to facilitate exploration of massive data. The miR-seq browser supports users to examine short read alignment with the secondary structure and read count information available in concurrent windows. Features such as sequence editing, sorting, ordering, import and export of user data would be of great utility for studying iso-miRs, miRNA editing and modifications. miRNA–target relation is essential for understanding miRNA function. Coexpression analysis of miRNA and target mRNAs, based on miRNA-seq and RNA-seq data from the same sample, is visualized in the heat-map and network views where users can investigate the inverse correlation of gene expression and target relations, compiled from various databases of predicted and validated targets. By keeping datasets and analytic tools up-to-date, miRGator should continue to serve as an integrated resource for biogenesis and functional investigation of miRNAs.
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影响因子：
14.9
作者：
Kozomara A;Griffiths-Jones S
通讯作者：
Griffiths-Jones S
影响因子：
14.9
作者：
Xu J;Li CX;Li YS;Lv JY;Ma Y;Shao TT;Xu LD;Wang YY;Du L;Zhang YP;Jiang W;Li CQ;Xiao Y;Li X
通讯作者：
Li X
影响因子：
14.9
作者：
Xiao F;Zuo Z;Cai G;Kang S;Gao X;Li T
通讯作者：
Li T
影响因子：
14.9
作者：
Betel D;Wilson M;Gabow A;Marks DS;Sander C
通讯作者：
Sander C
影响因子：
14.9
作者：
Barrett T;Troup DB;Wilhite SE;Ledoux P;Evangelista C;Kim IF;Tomashevsky M;Marshall KA;Phillippy KH;Sherman PM;Muertter RN;Holko M;Ayanbule O;Yefanov A;Soboleva A
通讯作者：
Soboleva A