DIANA Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece.
Hellenic Pasteur Institute, 11521 Athens, Greece.
Genes (Basel). 2020 Dec 30;12(1):46. doi: 10.3390/genes12010046.
microRNAs (miRNAs) are small non-coding RNAs (~22 nts) that are considered central post-transcriptional regulators of gene expression and key components in many pathological conditions. Next-Generation Sequencing (NGS) technologies have led to inexpensive, massive data production, revolutionizing every research aspect in the fields of biology and medicine. Particularly, small RNA-Seq (sRNA-Seq) enables small non-coding RNA quantification on a high-throughput scale, providing a closer look into the expression profiles of these crucial regulators within the cell. Here, we present DIANA-microRNA-Analysis-Pipeline (DIANA-mAP), a fully automated computational pipeline that allows the user to perform miRNA NGS data analysis from raw sRNA-Seq libraries to quantification and Differential Expression Analysis in an easy, scalable, efficient, and intuitive way. Emphasis has been given to data pre-processing, an early, critical step in the analysis for the robustness of the final results and conclusions. Through modularity, parallelizability and customization, DIANA-mAP produces high quality expression results, reports and graphs for downstream data mining and statistical analysis. In an extended evaluation, the tool outperforms similar tools providing pre-processing without any adapter knowledge. Closing, DIANA-mAP is a freely available tool. It is available dockerized with no dependency installations or standalone, accompanied by an installation manual through Github.
微小 RNA（miRNAs）是一种小的非编码 RNA（~22 个核苷酸），被认为是基因表达的中心转录后调控因子，也是许多病理条件的关键组成部分。下一代测序（NGS）技术导致了廉价、海量数据的产生，彻底改变了生物学和医学领域的各个研究方面。特别是，小 RNA-Seq（sRNA-Seq）能够在高通量水平上对小非编码 RNA 进行定量，更深入地了解这些关键调控因子在细胞内的表达谱。在这里，我们介绍 DIANA-microRNA-Analysis-Pipeline（DIANA-mAP），这是一个完全自动化的计算流程，允许用户以简单、可扩展、高效和直观的方式从原始 sRNA-Seq 文库中执行 miRNA NGS 数据分析，进行定量和差异表达分析。我们强调了数据预处理，这是分析中的一个早期、关键步骤，对于最终结果和结论的稳健性至关重要。通过模块化、并行化和定制化，DIANA-mAP 为下游数据挖掘和统计分析生成高质量的表达结果、报告和图形。在扩展评估中，该工具的表现优于提供无适配器知识的预处理的类似工具。总之，DIANA-mAP 是一个免费的工具。它可以通过 Docker 进行无依赖安装或独立使用，同时提供了一个安装手册，可通过 Github 访问。
