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Published on: February 7, 2018
Identification the Low Oxidative Stress Subtype of Periodontitis
Yuchen Wu1, Xianfang Zhang1, Yunong Chen1
1Department of Prosthodontics, Shanghai Xuhui District Dental Center, Shanghai, People's Republic of China.
Objective:
The aim of this research was to identify the low oxidative stress-related genes expression (L-OS) subtype in patients with periodontitis.
Methods:
Microarray data (MA) were retrieved from the Gene Expression Omnibus database. The different oxidative stress (OS) subtypes of periodontitis were identified by K-means clustering analysis and gene set variation analysis (GSVA). Differentially expressed genes (DEGs) (|Log fold change (FC)| >1, q < 0.05) amongst the OS subtypes and healthy controls (HCs) were identified by Limma R package. The genomic feature of L-OS subtype and corresponding medicines were evaluated and visualised with Drug-Gene Interaction Database and cytoscape-v3.7.2 software (Pearson correlation coefficient > 0.4). Finally, the LASSO-Logistic regression model was adopted to evaluate and predict patients' OS phenotype in routine clinical practice.
Results:
The 241 periodontitis samples and 69 HCs were included. Thirty-three DEGs between the L-OS and high oxidative stress-related genes expression (H-OS) subtypes and 96 DEGs, including 8 transcription factors, between L-OS subtype and HCs were identified, respectively. Then, the network of TFs-Genes-Drugs was constructed to determine genomic feature of L-OS subtype. Finally, a 4-gene signature formula and the cutoff value were identified by ML with LASSO model to predict patients' classification.
Conclusions:
For the first time, we identified L-OS subtype of periodontitis and evaluated its genomic feature with MA.
