A gene pathway enrichment method based on improved TF-IDF algorithm(PDF)
《中国医学物理学杂志》[ISSN:1005-202X/CN:44-1351/R]
- Issue:
- 2022年第9期
- Page:
- 1173-1181
- Research Field:
- 其他（激光医学等）
- Publishing date:
Info
- Title:
- A gene pathway enrichment method based on improved TF-IDF algorithm
- Author(s):
- XU Shutan1; 2; LENG Yinhui1; 2; CHEN Ming1; 2
- 1. College of Information Technology, Shanghai Ocean University, Shanghai 201306, China 2.Key Laboratory of Fisheries Information, Ministry of Agriculture and Rural Affairs of the Peoples Republic of China, Shanghai 201306, China
- Keywords:
- pathway enrichment genet impact gene set enrichment analysis
- PACS:
- R318
- DOI:
- DOI:10.3969/j.issn.1005-202X.2022.09.019
- Abstract:
- A gene pathway enrichment method (GIGSEA method) that comprehensively considers the local and global information of the pathways is proposed. The gene interaction data are used to calculate the gene impact based on the local importance of the gene in the pathway and its global specificity in the pathway database. Then the obtained gene impact is fused with the phenotypic correlation value to calculate enrichment score, and statistically significant pathways are identified by permutating gene. GIGSEA is applied to the data sets of hepatocellular carcinoma and colorectal cancer for the enrichment of risk pathways. Compared with the gene set enrichment analysis method, GIGSEA method can enrich some new related pathways and exclude irrelevant pathways, which improves the enrichment effect of disease-associated pathways.
Last Update: 2022-09-27