Identification of Type 2 Diabetes Based on a Ten-Gene Biomarker Prediction Model Constructed Using a Support Vector Machine Algorithm

Abstract

Background. Type 2 diabetes is a major health concern worldwide. The present study is aimed at discovering effective biomarkers for an efficient diagnosis of type 2 diabetes. Methods. Differentially expressed genes (DEGs) between type 2 diabetes patients and normal controls were identified by analyses of integrated microarray data obtained from the Gene Expression Omnibus database using the Limma package. Functional analysis of genes was performed using the R software package clusterProfiler. Analyses of protein-protein interaction (PPI) performed using Cytoscape with the CytoHubba plugin were used to determine the most sensitive diagnostic gene biomarkers for type 2 diabetes in our study. The support vector machine (SVM) classification model was used to validate the gene biomarkers used for the diagnosis of type 2 diabetes. Results. GSE164416 dataset analysis revealed 499 genes that were differentially expressed between type 2 diabetes patients and normal controls, and these DEGs were found to be enriched in the regulation of the immune effector pathway, type 1 diabetes mellitus, and fatty acid degradation. PPI analysis data showed that five MCODE clusters could be considered as clinically significant modules and that 10 genes (IL1B, ITGB2, ITGAX, COL1A1, CSF1, CXCL12, SPP1, FN1, C3, and MMP2) were identified as “real” hub genes in the PPI network using algorithms such as Degree, MNC, and Closeness. The sensitivity and specificity of the SVM model for identifying patients with type 2 diabetes were 100%, with an area under the curve of 1 in the training as well as the validation dataset. Conclusion. Our results indicate that the SVM-based model developed by us can facilitate accurate diagnosis of type 2 diabetes.