An Improved Network-Enhanced Fusion Method and its Application in Papillary Renal Cell Carcinoma Subtyping using Multi-omics Data
10.11783/j.issn.1002-3674.2024.03.010
- VernacularTitle:网络增强核融合方法的改进及其在乳头状肾细胞癌多组学数据整合分子分型中的应用
- Author:
Guojing SHI
1
;
Lingmei LI
;
Yifang WEI
Author Information
1. 山西医科大学卫生统计教研室(030001)
- Keywords:
Improved ne-SNF;
Papillary renal cell carcinoma;
Multi-omics data integration;
Molecular subtyping
- From:
Chinese Journal of Health Statistics
2024;41(3):376-381
- CountryChina
- Language:Chinese
-
Abstract:
Objective The Network Enhancement Fusion(ne-SNF)method had no denoising strategy for the networks from each omics data type,which would weaken the power of network fusion.To address this problem,we proposed an improved Network Enhancement Fusion(improved ne-SNF)model,and further applied the method to subtype identification of papillary renal cell carcinoma.Methods We conducted simulation studies to compare the performances of the improved ne-SNF method with the ne-SNF and SNF method,and applied improved ne-SNF method to integrate multi-omics data of PRCC.Cox regression model was performed to evaluate the prognostic risk of different subtypes.Differentially expressed mRNAs(DEmRNAs),miRNAs(DEmiRNAs)and differentially methylated genes(DMGs)with different subtypes were screened.KEGG pathway analysis was performed for the overlapping genes of three gene sets.Finally,the immune cell infiltration analysis was performed for patients with different subtypes.Results The improved ne-SNF method outperformed both SNF and ne-SNF approach in various simulation scenarios.In subsequent subtyping application,PRCC patients were divided into high-risk and low-risk groups,and the risk of death was 7.727 times higher in the high-risk group than in the low-risk group.A total of 3511 DEmRNAs,96 DEmiRNAs and 3426 DMGs were identified.Among them,649 overlapping genes yielded 42 KEGG pathways with statistical differences.In addition,3 immune filtrating cells showed statistical significance.Conclusion The improved ne-SNF performed better than SNF and ne-SNF,and the identified subtypes of PRCC may provide important clues and basis for treatment of PRCC patient.
