Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, California 94010, USA.
Pharm Res. 2012 Jul;29(7):1717-21. doi: 10.1007/s11095-012-0712-x. Epub 2012 Feb 24.
Understanding the regulation of gene expression is critical to many areas of biology while control via RNAs has found considerable interest as a tool for scientific discovery and potential therapeutic applications. For example whole genome RNA interference (RNAi) screens and whole proteome scans provide views of how the entire transcriptome or proteome responds to biological, chemical or environmental perturbations of a gene's activity. Small RNA (sRNA) or MicroRNA (miRNA) are known to regulate pathways and bind mRNA, while the function of miRNAs discovered in experimental studies is often unknown. In both cases, RNAi and miRNA require labor intensive studies to tease out their functions within gene networks. Available software to analyze relationships is currently an ad hoc and often a manual process that can take up to several hours to analyze a single candidate RNAi or miRNA. With experiments frequently highlighting tens to hundreds of candidates this represents a considerable bottleneck. We suggest there is a gap in miRNA and RNAi research caused by inadequate current software that could be improved. For example a new software application could be created that provides interactive, comprehensive target analysis that leverages past datasets to lead to statistically stronger analyses.
理解基因表达的调控对于生物学的许多领域都至关重要，而 RNA 的调控作为科学发现和潜在治疗应用的工具已经引起了相当大的关注。例如，全基因组 RNA 干扰 (RNAi) 筛选和全蛋白质组扫描提供了关于整个转录组或蛋白质组如何响应基因活性的生物学、化学或环境扰动的视图。小 RNA (sRNA) 或 MicroRNA (miRNA) 已知可以调节途径并与 mRNA 结合，而在实验研究中发现的 miRNA 的功能通常是未知的。在这两种情况下，RNAi 和 miRNA 都需要进行劳动密集型的研究，以梳理它们在基因网络中的功能。目前可用于分析关系的软件是一种临时的、通常是手动的过程，分析单个候选 RNAi 或 miRNA 可能需要数小时。由于实验经常突出数十到数百个候选者，这代表了一个相当大的瓶颈。我们认为，由于当前软件的不足，miRNA 和 RNAi 研究存在差距，这是可以改进的。例如，可以创建一个新的软件应用程序，提供交互式、全面的目标分析，利用过去的数据集进行更具统计学意义的分析。
