Xu Shutan, Leng Yinhui, Feng Guofu, Zhang Chenjing, Chen Ming
College of Information Technology, Shanghai Ocean University, Shanghai, 201306, China.
Key Laboratory of Fisheries Information, Ministry of Agriculture, Shanghai, 201306, China.
Biochem Biophys Rep. 2023 Mar 6;34:101421. doi: 10.1016/j.bbrep.2023.101421. eCollection 2023 Jul.
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.
基因通路富集分析是一种广泛使用的方法，用于分析基因集在特定生物通路网络上是否存在统计学富集。当前的基因通路富集方法通常考虑基因在通路中的局部重要性，而不考虑基因之间的相互作用。在本文中，我们提出了一种基于改进的TF-IDF算法的基因通路富集方法（GIGSEA）。该方法利用基因相互作用数据，基于通路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，本文提出的方法能够更高效地找到与表型相关的更特定的富集通路。
