A Sparse and Low-Rank Regression Model for Identifying the Relationships Between DNA Methylation and Gene Expression Levels in Gastric Cancer and the Prediction of Prognosis

Genes

Dongmei Ai¹  Yishu Wang¹  Lingyun Xu² 

[1] School of Mathematics and Physics, University of Science & Technology Beijing, Beijing 100083, China;School of Mathematics and Statistics, Qingdao University, Qingdao 266003, China;

关键词: low-rank sparse regression model;    DNA methylation;    prognosis;    gene expression;    gastric cancer;   

DOI  :  10.3390/genes12060854

来源: DOAJ

【 摘 要 】

DNA methylation is an important regulator of gene expression that can influence tumor heterogeneity and shows weak and varying expression levels among different genes. Gastric cancer (GC) is a highly heterogeneous cancer of the digestive system with a high mortality rate worldwide. The heterogeneous subtypes of GC lead to different prognoses. In this study, we explored the relationships between DNA methylation and gene expression levels by introducing a sparse low-rank regression model based on a GC dataset with 375 tumor samples and 32 normal samples from The Cancer Genome Atlas database. Differences in the DNA methylation levels and sites were found to be associated with differences in the expressed genes related to GC development. Overall, 29 methylation-driven genes were found to be related to the GC subtypes, and in the prognostic model, we explored five prognoses related to the methylation sites. Finally, based on a low-rank matrix, seven subgroups were identified with different methylation statuses. These specific classifications based on DNA methylation levels may help to account for heterogeneity and aid in personalized treatments.

【 授权许可】

Unknown