Pantano Lorena, Pantano Francisco, Marti Eulalia, Ho Sui Shannan
Biostatistics, Harvard T.H. Chan school of Public Health, Boston, MA, 02115, USA.
Independent Researcher, San Juan, Argentina.
F1000Res. 2019 Feb 28;8. doi: 10.12688/f1000research.18142.2. eCollection 2019.
The study of small RNAs provides us with a deeper understanding of the complexity of gene regulation within cells. Of the different types of small RNAs, the most important in mammals are miRNA, tRNA fragments and piRNAs. Using small RNA-seq analysis, we can study all small RNA types simultaneously, with the potential to detect novel small RNA types. We describe SeqclusterViz, an interactive HTML-javascript webpage for visualizing small noncoding RNAs (small RNAs) detected by Seqcluster. The SeqclusterViz tool allows users to visualize known and novel small RNA types in model or non-model organisms, and to select small RNA candidates for further validation. SeqclusterViz is divided into three panels: i) query-ready tables showing detected small RNA clusters and their genomic locations, ii) the expression profile over the precursor for all the samples together with RNA secondary structures, and iii) the mostly highly expressed sequences. Here, we show the capabilities of the visualization tool and its validation using human brain samples from patients with Parkinson's disease.
对小RNA的研究使我们对细胞内基因调控的复杂性有了更深入的理解。在不同类型的小RNA中，哺乳动物中最重要的是miRNA、tRNA片段和piRNA。使用小RNA测序分析，我们可以同时研究所有类型的小RNA，有可能检测到新的小RNA类型。我们描述了SeqclusterViz，一个交互式HTML- javascript网页，用于可视化由Seqcluster检测到的小非编码RNA（小RNA）。SeqclusterViz工具允许用户可视化模型或非模型生物中已知和新的小RNA类型，并选择小RNA候选物进行进一步验证。SeqclusterViz分为三个面板：i）显示检测到的小RNA簇及其基因组位置的查询就绪表，ii）所有样本前体的表达谱以及RNA二级结构，iii）表达量最高的序列。在这里，我们展示了该可视化工具的功能及其使用帕金森病患者人脑样本进行的验证。
