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The real-time quantification of the number of amplified products is...
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Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
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InterOpt:在使用参考基因加权聚合的qPCR实验中改进了基因表达量化.

Adel Salimi1, Saeid Rahmani1,2, Ali Sharifi-Zarchi1

  • 1Computer Engineering Department, Sharif University of Technology, Tehran 11155-1639, Tehran, Iran.

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概括

定量PCR (qPCR) 的准确性依赖于参考基因 (RG) 的正常化. 这项研究引入了改进的RG聚合方法,优于精确基因表达分析的标准几何平均值.

关键词:
生物计算方法是一种生物计算方法.系统生物学中的数据处理.表达式研究研究.

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科学领域:

  • 分子生物学分子生物学
  • 生物信息学是一种生物信息学.
  • 基因组学就是基因组学.

背景情况:

  • 定量PCR (qPCR) 是基因表达量化的黄金标准.
  • 使用参考基因 (RG) 进行准确的正常化对于qPCR可靠性至关重要.
  • 目前用于汇总多个RG的方法往往缺乏最佳性能.

研究的目的:

  • 引入新的,规模不变的功能,用于在qPCR中聚合多个参考基因.
  • 将这些新聚合方法的性能与传统的几何平均值进行比较.
  • 为参考基因正常化提供计算效率高,适应性强的解决方案.

主要方法:

  • 开发一个用于RG聚合的规模不变函数家族.
  • 衡量几何平均值方法的评估,使标准偏差最小化.
  • 理论分析和实验验证,使用实体瘤和液体活检的现实数据.
  • 在带有GPU加速的R包中实施拟议的方法.

主要成果:

  • 拟议的权重几何平均值方法与现有的聚合技术相比,显示出更高的性能.
  • 尺度不变函数为RG规范化提供了对几何平均值的可靠替代方案.
  • 开发的R包使得正常化基因表达数据的有效和可访问的计算成为可能.

结论:

  • 新的RG聚合方法显著提高了qPCR的准确性.
  • 减小标准偏差的权重几何平均值是一个非常有效的方法.
  • 提供的R包有助于在基因表达研究中广泛采用改进的正常化策略.