A gene pathway enrichment method based on improved TF-IDF algorithm.

一种基于改进 TF - IDF 算法的基因通路富集方法

• 发表时间: Jul 2023
• 来源期刊: Biochem Biophys Rep
• DOI: 10.1016/j.bbrep.2023.101421
• PMID: 36923007
• 文章类型: Journal Article
• 作者列表: Xu S,Leng Y,Feng G,Zhang C,Chen M

关键词: Gene interaction; Gene set enrichment analysis; Pathway enrichment; TF-IDF

Abstract

Gene pathway enrichment analysis is a widely used method to analyze whether a gene set is statistically enriched on certain biological pathway network. Current gene pathway enrichment methods commonly consider local importance of genes in pathways without considering the interactions between genes. In this paper, we propose a gene pathway enrichment method (GIGSEA) based on improved TF-IDF algorithm. This method employs gene interaction data to calculate the influence of genes based on the local importance in a pathway as well as the global specificity. Computational experiment result shows that, compared with traditional gene set enrichment analysis method, our proposed method in this paper can find more specific enriched pathways related to phenotype with higher efficiency.

摘要

基因途径富集分析是一种广泛使用的方法，用于分析基因集是否在某些生物途径网络上进行统计富集。目前的基因途径富集方法通常考虑基因在途径中的局部重要性,而不考虑基因之间的相互作用。在本文中,提出了一种基于改进TF-IDF算法的基因途径富集方法(GIGSEA)。该方法使用基因相互作用数据来基于途径中的局部重要性以及全局特异性来计算基因的影响。计算实验结果表明,与传统的基因集富集分析方法相比，我们在本文中提出的方法可以以更高的效率找到与表型相关的更特异的富集途径。