Prediction of Hepatocellular Carcinoma Diseases Based on Methylation Data and Screening of Hub Genes

Abstract

DNA methylation is of great significance to the diagnosis, treatment and disease prediction of hepatocellular carcinoma (HCC). The commonly used DNA methylation microarrays have high data dimensions, and different CpG sites detected may map to the same gene. To extract more effective features for HCC disease prediction, this study uses a linear regression model that integrates TCGA database methylation data and gene expression data, based on the DNA methylation microarray data of the GEO database (GSE113017), the corresponding gene expression data was predicted and the differentially expressed genes (3766) with significant differences were screened out, which was used as the feature of the data set. Constructing an Artificial Neural Network (ANN) to train a machine learning model for HCC disease prediction and perform 10-fold cross-validation. The resulting model has an accuracy of 95.1% for HCC disease prediction based on DNA methylation microarray data. Compared with other HCC prediction methods, this method has better performance. Then analyze the differentially expressed genes with protein-protein interaction network (PPI network), and use the top five connected genes in the network as hub genes, namely: GNGT2, GNB4, FPR2, CDC20, NMUR1, which can be used as biomarkers for the diagnosis, treatment and prognosis of HCC.