PSF工具包:用于路径策划和拓意识分析的R包
Siras Hakobyan1,2, Ani Stepanyan3, Lilit Nersisyan2
1Bioinformatics Group, Institute of Molecular Biology, Armenian National Academy of Sciences, Yerevan, Armenia.
Frontiers in genetics
|September 8, 2023
概括
路径信号流 (PSF) 工具包R包通过将路径策划与以拓为基础的方法相结合,增强了基因组数据分析. 它提供了一种灵活,易于使用的方法,用于详细的通路信号流分析,改进了传统方法.
科学领域:
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
- 基因组学就是基因组学.
背景情况:
- 高通量基因组数据分析通常使用过度表示分析/基因组丰富分析 (ORA/GSEA).
- 基于拓学的路径分析虽然更具信息性,但由于路径拓学的可访问性和质量问题,其利用率不足.
研究的目的:
- 引入路径信号流 (PSF) 工具包R包,用于可访问和灵活的拓意识路径分析.
- 将路径策划与基于拓的分析整合在一起,解决现有方法的局限性.
主要方法:
- 开发了PSF工具包R包,其中包含交互式和命令行工具,用于路径导入,校正和修改.
- 策划了36个KEGG信号通路,并与ORA和信号通路影响分析 (SPIA) 进行了比较分析.
主要成果:
- 该PSF工具集有效地识别了ORA丰富的途径,并提供了分支机构级别的详细信息.
- 与SPIA相比,PSF分析是没有切断的,并且不太容易受到值变化的影响.
- 在拓意识路径分析中证明了提高质量,灵活性和可访问性.
结论:
- 该PSF工具包为路径修复和基于拓的信号流分析提供了一个集成的解决方案.
- 赋予研究人员在各种应用中进行全面的途径分析的工具.
- 改进了传统的ORA/GSEA和基于拓的方法,如SPIA.
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