Establishment and analysis of a disease risk prediction model for the systemic lupus erythematosus with random forest

作者：Huajian Chen, Huang Li, Xinyue Jiang, Yue Wang, Yan Bian, Shumei Ma, Xiaodong Liu · 发表于：Frontiers in Immunology · 年份：2022 · DOI：10.3389/fimmu.2022.1025688 · 被引用次数：18 · 研究领域：Systemic Lupus Erythematosus Research、Atherosclerosis and Cardiovascular Diseases、Liver Disease Diagnosis and Treatment

Systemic lupus erythematosus (SLE) is a latent, insidious autoimmune disease, and with the development of gene sequencing in recent years, our study aims to develop a gene-based predictive model to explore the identification of SLE at the genetic level. First, gene expression datasets of SLE whole blood samples were collected from the Gene Expression Omnibus (GEO) database. After the datasets were merged, they were divided into training and validation datasets in the ratio of 7:3, where the SLE samples and healthy samples of the training dataset were 334 and 71, respectively, and the SLE samples and healthy samples of the validation dataset were 143 and 30, respectively. The training dataset was used to build the disease risk prediction model, and the validation dataset was used to verify the model identification ability. We first analyzed differentially expressed genes (DEGs) and then used Lasso and random forest (RF) to screen out six key genes (OAS3, USP18, RTP4, SPATS2L, IFI27 and OAS1), which are essential to distinguish SLE from healthy samples. With six key genes incorporated and five iterations of 10-fold cross-validation performed into the RF model, we finally determined the RF model with optimal mtry. The mean values of area under the curve (AUC) and accuracy of the models were over 0.95. The validation dataset was then used to evaluate the AUC performance and our model had an AUC of 0.948. An external validation dataset (GSE99967) with an AUC of 0.810, an accuracy ...