sRNATargetDigger: A bioinformatics software for bidirectional identification of sRNA-target pairs with co-regulatory sRNAs information.
sRNATargetDigger: A bioinformatics software for bidirectional identification of sRNA-target pairs with co-regulatory sRNAs information.
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sRNATargetDigger：一种生物信息学软件，用于通过共调节 sRNA 信息双向识别 sRNA-靶标对
DOI：
10.1371/journal.pone.0244480
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发表时间：
2020
期刊：
影响因子：
3.7
通讯作者：
Shao C
中科院分区：
文献类型：
--
作者：
Ye X;Yang Z;Jiang Y;Yu L;Guo R;Meng Y;Shao C
鉴定microRNAs(MiRNAs)、反式作用小干扰RNAs(ta-siRNAs)和小干扰RNAs(SiRNAs)的靶基因是了解它们在植物中的调控作用的重要一步。近年来，许多基于小RNA(SRNA)高通量测序(HTS)和降解基因组测序数据分析的生物信息学软件包为大规模挖掘sRNA-靶点对提供了强有力的技术支持。然而，sRNA-靶调控是使用复杂的相互作用网络实现的，因为一个转录本可能受到多个sRNA的共同调控，并且一个sRNA也可能影响多个靶。目前使用的挖掘软件可以利用已知的sRNA实现对多个未知目标的挖掘，但不能排除其他未知sRNA共同调控同一目标的可能性。因此，获得的监管网络可能是不完整的。我们开发了一个新的挖掘软件sRNatargetDigger，它包括两个功能模块：正向挖掘器和反向挖掘器，可以双向识别调控的sRNA-靶对。此外，它还具有识别共同调节同一靶标的未知sRNA的能力，以获得更真实和可靠的sRNA靶标调控网络。在重新检查已发表的拟南芥sRNA-靶标对后，sRNatargetDigger发现了170个新的共调控的sRNA-靶标对。该软件可从http://www.bioinfolab.cn/sRNATD.html.下载
Identification of the target genes of microRNAs (miRNAs), trans-acting small interfering RNAs (ta-siRNAs), and small interfering RNAs (siRNAs) is an important step for understanding their regulatory roles in plants. In recent years, many bioinformatics software packages based on small RNA (sRNA) high-throughput sequencing (HTS) and degradome sequencing data analysis have provided strong technical support for large-scale mining of sRNA-target pairs. However, sRNA-target regulation is achieved using a complex network of interactions since one transcript might be co-regulated by multiple sRNAs and one sRNA may also affect multiple targets. Currently used mining software can realize the mining of multiple unknown targets using known sRNA, but it cannot rule out the possibility of co-regulation of the same target by other unknown sRNAs. Hence, the obtained regulatory network may be incomplete. We have developed a new mining software, sRNATargetDigger, that includes two function modules, “Forward Digger” and “Reverse Digger”, which can identify regulatory sRNA-target pairs bidirectionally. Moreover, it has the ability to identify unknown sRNAs co-regulating the same target, in order to obtain a more authentic and reliable sRNA-target regulatory network. Upon re-examination of the published sRNA-target pairs in Arabidopsis thaliana, sRNATargetDigger found 170 novel co-regulatory sRNA-target pairs. This software can be downloaded from http://www.bioinfolab.cn/sRNATD.html.
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影响因子：
4.6
作者：
Mutum RD;Kumar S;Balyan S;Kansal S;Mathur S;Raghuvanshi S
通讯作者：
Raghuvanshi S
影响因子：
11.8
作者：
Gregory, Brian D.;O'Malley, Ronan C.;Ecker, Joseph R.
通讯作者：
Ecker, Joseph R.
影响因子：
9.2
作者：
Addo-Quaye, Charles;Eshoo, Tifani W.;Axtell, Michael J.
通讯作者：
Axtell, Michael J.
DOI：
10.1007/978-1-61779-083-6_11
发表时间：
2011-01-01
期刊：
MICRORNAS IN DEVELOPMENT: METHODS AND PROTOCOLS
影响因子：
--
作者：
Nicolas, Francisco E.
通讯作者：
Nicolas, Francisco E.
影响因子：
5.8
作者：
Addo-Quaye, Charles;Miller, Webb;Axtell, Michael J.
通讯作者：
Axtell, Michael J.