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Updated: Sep 27, 2025
Robust Ligature-Induced Model of Murine Periodontitis for the Evaluation of Oral Neutrophils
Published on: January 21, 2020
Identification of microRNA-mRNA-TF regulatory networks in periodontitis by bioinformatics analysis
Xiaoli Gao1, Dong Zhao1, Jing Han1
1Department of Stomatology, Beijing Chaoyang Hospital, Capital Medical University, 8 Gongti Nan Lu, Chaoyang District, Beijing, 100020, China.
Background:
Periodontitis is a complex infectious disease with various causes and contributing factors. The aim of this study was to identify key genes, microRNAs (miRNAs) and transcription factors (TFs) and construct a miRNA-mRNA-TF regulatory networks to investigate the underlying molecular mechanism in periodontitis.
Methods:
The GSE54710 miRNA microarray dataset and the gene expression microarray dataset GSE16134 were downloaded from the Gene Expression Omnibus database. The differentially expressed miRNAs (DEMis) and mRNAs (DEMs) were screened using the "limma" package in R. The intersection of the target genes of candidate DEMis and DEMs were considered significant DEMs in the regulatory network. Next, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted. Subsequently, DEMs were uploaded to the STRING database, a protein-protein interaction (PPI) network was established, and the cytoHubba and MCODE plugins were used to screen out key hub mRNAs and significant modules. Ultimately, to investigate the regulatory network underlying periodontitis, a global triple network including miRNAs, mRNAs, and TFs was constructed using Cytoscape software.
Results:
8 DEMis and 121 DEMs were found between the periodontal and control groups. GO analysis showed that mRNAs were most significantly enriched in positive regulation of the cell cycle, and KEGG pathway analysis showed that mRNAs in the regulatory network were mainly involved in the IL-17 signalling pathway. A PPI network was constructed including 81 nodes and 414 edges. Furthermore, 12 hub genes ranked by the top 10% genes with high degree connectivity and five TFs, including SRF, CNOT4, SIX6, SRRM3, NELFA, and ONECUT3, were identified and might play crucial roles in the molecular pathogenesis of periodontitis. Additionally, a miRNA-mRNA-TF coregulatory network was established.
Conclusion:
In this study, we performed an integrated analysis based on public databases to identify specific TFs, miRNAs, and mRNAs that may play a pivotal role in periodontitis. On this basis, a TF-miRNA-mRNA network was established to provide a comprehensive perspective of the regulatory mechanism networks of periodontitis.
Insights
This study identifies key genes, microRNAs, and transcription factors involved in periodontitis pathogenesis. A regulatory network highlights their crucial roles in this complex infectious disease.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Periodontitis is a complex infectious disease with multifactorial causes.
- Understanding its molecular mechanisms is crucial for effective treatment strategies.
Purpose of the Study:
- To identify key genes, microRNAs (miRNAs), and transcription factors (TFs) in periodontitis.
- To construct a comprehensive miRNA-mRNA-TF regulatory network for periodontitis.
Main Methods:
- Utilized public datasets (GSE54710, GSE16134) for miRNA and mRNA expression analysis.
- Applied bioinformatics tools (limma, STRING, Cytoscape) to identify differentially expressed molecules, construct protein-protein interaction networks, and build a regulatory network.
- Performed Gene Ontology and KEGG pathway enrichment analyses.
Main Results:
- Identified 8 differentially expressed miRNAs (DEMis) and 121 differentially expressed mRNAs (DEMs).
- Key pathways identified include positive regulation of the cell cycle and the IL-17 signaling pathway.
- A coregulatory network of miRNA-mRNA-TF was established, highlighting 12 hub genes and 5 crucial TFs (SRF, CNOT4, SIX6, SRRM3, NELFA, ONECUT3).
Conclusions:
- Integrated analysis identified pivotal TFs, miRNAs, and mRNAs in periodontitis.
- The established TF-miRNA-mRNA network offers a comprehensive view of periodontitis regulatory mechanisms.
