Using bioinformatics analysis to screen abnormal methylated differentially expressed hub genes of Kawasaki disease and construct diagnostic model

Hongxiao Sun; Changying Liu; Xu Zhang; Panpan Liu; Zhanhui Du; Gang Luo; Silin Pan

doi:10.1016/j.heliyon.2022.e11905

Using bioinformatics analysis to screen abnormal methylated differentially expressed hub genes of Kawasaki disease and construct diagnostic model

Heliyon. 2022 Nov 25;8(11):e11905. doi: 10.1016/j.heliyon.2022.e11905. eCollection 2022 Nov.

Authors

Hongxiao Sun¹, Changying Liu², Xu Zhang³, Panpan Liu¹, Zhanhui Du¹, Gang Luo¹, Silin Pan¹

Affiliations

¹ Heart Center, Women and Children's Hospital, Qingdao University, 266034 Qingdao, China.
² Rehabilitation Medicine Department, Women and Children's Hospital, Qingdao University, 266034 Qingdao, China.
³ Anesthesiology Department, Women and Children's Hospital, Qingdao University, 266034 Qingdao, China.

Abstract

Objective: By using bioinformatics analysis, abnormal methylated differentially expressed genes (MDEGs) in Kawasaki disease (KD) were identified and a random forest diagnostic model for KD was established.

Methods: The expression (GSE18606, GSE68004, GSE73461) and methylation (GSE109430) profiles was retrieved and download from Gene Expression Omnibus (GEO). We conducted enrichment analyses by using R software. In addition, we constructed a protein interaction network, and obtained 6 hub genes. We used expression profiles GSE100154 from GEO to verify the hub genes. Finally, we constructed a diagnostic model based on random forest.

Results: We got a total of 55 MDEGs (43 hyper-methylated, low-expressing genes and 12 hypo-methylated, high-expressed genes). Six hub genes (CD2, IL2RB, IL7R, CD177, IL1RN, and MYL9) were identified by Cytoscape software. The area under curve (AUC) of the six hub genes was from 0.745 to 0.898, and the combined AUC was 0.967. The random forest diagnostic model showed that AUC was 0.901.

Conclusion: The identification of 6 new hub genes improves our understanding of the molecular mechanism of KD, and the established model can be employed for accurate diagnosis and provide evidence for clinical diagnosis.

Keywords: Differentially expressed genes; Gene expression omnibus; Kawasaki disease; Protein-protein interaction network; Random forest.