isomiRs-Hidden Soldiers in the miRNA Regulatory Army, and How to Find Them?
isomiRs-Hidden Soldiers in the miRNA Regulatory Army, and How to Find Them?
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DOI：
10.3390/biom11010041
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发表时间：
2020-12-30
期刊：
影响因子：
5.5
通讯作者：
Baev V
中科院分区：
文献类型：
--
作者：
Glogovitis I;Yahubyan G;Würdinger T;Koppers-Lalic D;Baev V
关于癌症和其他疾病中微小RNA（miRNA）的众多研究伴随着多种计算方法和实验方法来预测和验证miRNA作为易于获得的疾病生物标志物的生物学和临床意义。近年来，下一代深度测序用于分析和发现新的RNA生物标志物的应用已经清楚地显示了成熟miRNA或isomiR的不同序列变体的不断扩大的库，这些变体由替代的转录后加工事件引起，并且受到（病理）生理变化、群体起源、个体性别和年龄的影响。在这里，我们提供了一个深入的概述，目前可用的生物信息学方法的检测和可视化的成熟的miRNA和同源isomiR序列。已经尝试以系统的方式呈现计算机模拟方法在其灵敏度和准确性性能方面的优点和缺点，以及所使用的方法，工作流程和处理步骤，以及最终输出数据集重叠问题。重点是给予的挑战和陷阱的isomiR表达分析。具体来说，我们解决了工具的可用性，使研究没有广泛的生物信息学背景，探索这个迷人的角落的小RNAome宇宙，可能有助于发现新的和更可靠的疾病生物标志物。
Numerous studies on microRNAs (miRNA) in cancer and other diseases have been accompanied by diverse computational approaches and experimental methods to predict and validate miRNA biological and clinical significance as easily accessible disease biomarkers. In recent years, the application of the next-generation deep sequencing for the analysis and discovery of novel RNA biomarkers has clearly shown an expanding repertoire of diverse sequence variants of mature miRNAs, or isomiRs, resulting from alternative post-transcriptional processing events, and affected by (patho)physiological changes, population origin, individual’s gender, and age. Here, we provide an in-depth overview of currently available bioinformatics approaches for the detection and visualization of both mature miRNA and cognate isomiR sequences. An attempt has been made to present in a systematic way the advantages and downsides of in silico approaches in terms of their sensitivity and accuracy performance, as well as used methods, workflows, and processing steps, and end output dataset overlapping issues. The focus is given to the challenges and pitfalls of isomiR expression analysis. Specifically, we address the availability of tools enabling research without extensive bioinformatics background to explore this fascinating corner of the small RNAome universe that may facilitate the discovery of new and more reliable disease biomarkers.
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影响因子：
3.7
作者：
Baras AS;Mitchell CJ;Myers JR;Gupta S;Weng LC;Ashton JM;Cornish TC;Pandey A;Halushka MK
通讯作者：
Halushka MK
影响因子：
3.7
作者：
Babapoor S;Fleming E;Wu R;Dadras SS
通讯作者：
Dadras SS
影响因子：
5.8
作者：
Bofill-De Ros, Xavier;Chen, Kevin;Gu, Shuo
通讯作者：
Gu, Shuo
影响因子：
64.8
作者：
Burns, David M.;D'Ambrogio, Andrea;Nottrott, Stephanie;Richter, Joel D.
通讯作者：
Richter, Joel D.
DOI：
10.1126/science.1190809
发表时间：
2010-06-25
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Cifuentes D;Xue H;Taylor DW;Patnode H;Mishima Y;Cheloufi S;Ma E;Mane S;Hannon GJ;Lawson ND;Wolfe SA;Giraldez AJ
通讯作者：
Giraldez AJ