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Bottlenecks Caused by Software Gaps in miRNA and RNAi Research

机译：miRNA和RNAi研究中软件空白导致的瓶颈

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摘要

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.
机译：理解基因表达的调控对生物学的许多领域至关重要，而通过RNA进行控制已引起人们极大的兴趣，作为科学发现和潜在治疗应用的工具。例如，全基因组RNA干扰（RNAi）筛查和整个蛋白质组扫描可提供有关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。已知小RNA（sRNA）或微RNA（miRNA）调节途径并结合mRNA，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研究，以阐明它们在基因网络中的功能。当前，用于分析关系的可用软件是临时的，通常是手动过程，可能需要花费几个小时才能分析单个候选RNAi或miRNA。随着实验频繁地突出显示数十到数百个候选者，这代表了相当大的瓶颈。我们建议miRNA和RNAi研究存在差距，这是由于当前软件不足而可以改进的。例如，可以创建一个新的软件应用程序，以提供交互式，全面的目标分析，该分析利用过去的数据集进行统计上更强的分析。

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  • 来源
    《Pharmaceutical Research》 |2012年第7期|p.1717-1721|共5页
  • 作者

    Sean Ekins; Ron Shigeta; Barry A. Bunin;

  • 作者单位

    Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, California, 94010, USA;

    Affymetrix, Inc., 6550 Vallejo Street, Suite 100, Emeryville, California, 94608, USA;

    Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, California, 94010, USA;

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  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

    informatics; microRNA; screening; siRNA; software;

    机译：信息学;microRNA;筛选;siRNA;软件;

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