Identification of hub genes and transcription factors involved in periodontitis on the basis of multiple microarray analysis.

Xiao Li Zeng; Sheng Jiao LI; Zheng Nan Shan; Jun Hao Yin; Ji Rui Jiang; Zhang Long Zheng; Jia LI

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Identification of hub genes and transcription factors involved in periodontitis on the basis of multiple microarray analysis.

Author: Xiao Li ZENG ^{1
,

2} ; Sheng Jiao LI ^{1
,

2} ; Zheng Nan SHAN ^{1
,

2} ; Jun Hao YIN ^{1
,

2} ; Ji Rui JIANG ^{1
,

2} ; Zhang Long ZHENG ^{1
,

2} ; Jia LI ^{1
,

3}
Author Information

1. Shanghai Engineering Research Center of Tooth Restoration and Regeneration
2. Dept. of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Tongji University, Shanghai 200072, China.
3. Dept. of Prosthodontics, School and Hospital of Stomatology, Tongji University, Shanghai 200072, China.
Publication Type:Journal Article
Keywords: bioinformatics analysis; differentially expressed genes; gene expression omnibus database; periodontitis
MeSH: Computational Biology; Gene Expression Profiling; Humans; Microarray Analysis; Periodontitis; Protein Interaction Maps
From: West China Journal of Stomatology 2021;39(6):633-641
CountryChina
Language:English
Abstract: OBJECTIVES:To identify the differentially expressed genes (DEGs) during the pathogenesis of periodontitis by bioinformatics analysis.
METHODS:GEO2R was used to screen DEGs in GSE10334 and GSE16134. Then, the overlapped DEGs were used for further analysis. g:Profiler was used to perform Gene Ontology analysis and pathway analysis for upregulated and downregulated DEGs. The STRING database was used to construct the protein-protein interaction (PPI) network, which was further visua-lized and analyzed by Cytoscape software. Hub genes and key modules were identified by cytoHubba and MCODE plug-ins, respectively. Finally, transcription factors were predicted via iRegulon plug-in.
RESULTS:A total of 196 DEGs were identified, including 139 upregulated and 57 downregulated DEGs. Functional enrichment analysis showed that the upregulated DEGs were mainly enriched in immune-related pathways including immune system, viral protein interaction with cytokine and cytokine receptor, cytokine-cytokine receptor interaction, leukocyte transendothelial migration, and chemokine receptors bind chemokines. On the contrary, the downregulated DEGs were mainly related to the formation of the cornified envelope and keratinization. The identified hub genes in the PPI network were CXCL8, CXCL1, CXCR4, SEL, CD19, and IKZF1. The top three modules were involved in chemokine response, B cell receptor signaling pathway, and interleukin response, respectively. iRegulon analysis revealed that IRF4 scored the highest.
CONCLUSIONS:The pathogenesis of periodontitis was closely associated with the expression levels of the identified hub genes including CXCL8, CXCL1, CXCR4, SELL, CD19, and IKZF1. IRF4, the predicted transcription factor, might serve as a dominant upstream regulator.