Cerulo Luigi, Pagnotta Stefano Maria
Department of Science and Technology, Università degli Studi del Sannio, 82100 Benevento, Italy.
Bioinformatics Lab, Biogem, Molecular Biology and Genetics Research Institute, 83031 Ariano Irpino, Italy.
Entropy (Basel). 2022 May 23;24(5):739. doi: 10.3390/e24050739.
Gene-set enrichment analysis is the key methodology for obtaining biological information from transcriptomic space's statistical result. Since its introduction, Gene-set Enrichment analysis methods have obtained more reliable results and a wider range of application. Great attention has been devoted to global tests, in contrast to competitive methods that have been largely ignored, although they appear more flexible because they are independent from the source of gene-profiles. We analyzed the properties of the Mann-Whitney-Wilcoxon test, a competitive method, and adapted its interpretation in the context of enrichment analysis by introducing a Normalized Enrichment Score that summarize two interpretations: a probability estimate and a location index. Two implementations are presented and compared with relevant literature methods: an R package and an online web tool. Both allow for obtaining tabular and graphical results with attention to reproducible research.
基因集富集分析是从转录组空间统计结果中获取生物学信息的关键方法。自引入以来，基因集富集分析方法已获得更可靠的结果和更广泛的应用。人们对全局检验给予了极大关注，与之形成对比的是，竞争方法在很大程度上被忽视了，尽管竞争方法似乎更灵活，因为它们独立于基因谱来源。我们分析了一种竞争方法——曼-惠特尼-威尔科克森检验的特性，并通过引入归一化富集分数（Normalized Enrichment Score）在富集分析的背景下调整了对其的解释，该分数总结了两种解释：概率估计和位置指数。本文给出了两种实现方式，并与相关文献方法进行了比较：一个R包和一个在线网络工具。两者都能获取表格和图形结果，并注重可重复性研究。
