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

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.