Identification of key module and hub genes in pulpitis using weighted gene co-expression network analysis

Zhang, Denghui; Zheng, Chao; Zhu, Tianer; Yang, Fan; Zhou, Yiqun

doi:10.1186/s12903-022-02638-9

Cited by 4 publications

(1 citation statement)

References 45 publications

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“…The Wnt signaling pathway regulates cell proliferation, differentiation, and tissue patterning for tooth development [ 10 - 12 ]. It plays a role in dental epithelial cell fate determination, tooth germ formation, tooth morphogenesis, and dental stem cell maintenance [ 13 ]. A comprehensive analysis method like WGCNA can be employed to understand the molecular mechanisms underlying Wnt signaling in odontogenic tissue formation.…”

Section: Introductionmentioning

confidence: 99%

Weighted Gene Co-expression Network Analysis (WGCNA) of Wnt Signaling Related to Periodontal Ligament Formation: A Bioinformatics-Based Analysis

Yadalam,

Ramadoss,

Arumuganainar

2024

Cureus

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Introduction The Wnt signaling pathway is crucial for tooth development, odontoblast differentiation, and dentin formation. It interacts with epithelial cadherin (E-cadherin) and beta-catenin in tooth development and periodontal ligament (PDL) formation. Dysregulation of Wnt signaling is linked to periodontal diseases, requiring an understanding of therapeutic interventions. Weighted gene co-expression network analysis (WGCNA) can identify co-expressed gene modules. Our study aims to identify hub genes in WGCNA analysis of Wnt signaling-based PDL formation. Methods The study used a microarray dataset GSE201313 from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus to analyze the impact of DMP1 expression on XLH dental pulp cell differentiation and PDL formation. The standardized dataset was used for WGCNA analysis, which generated a co-expression network by calculating pairwise correlations between genes and constructing an adjacency matrix. The topological overlap matrix (TOM) was transformed into a hierarchical clustering tree and then cut into modules or clusters of highly interconnected genes. The module eigengene (ME) was calculated for each module, and the genes within this module were identified as hub genes. Gene ontology (GO) and KEGG pathway enrichment analysis were performed to gain insights into the biological functions of the hub genes. The integrated Differential Expression and Pathway analysis (iDEP) tool ( http://bioinformatics.sdstate.edu/idep /; South Dakota State University, Brookings, USA) was used for WGCNA analysis. Results The study used the WGCNA package to analyze 1,000 differentially expressed genes, constructing a gene co-expression network and generating a hierarchical clustering tree and TOM. The analysis reveals a scale-free topology fitting index R2 and mean connectivity for various soft threshold powers, with an R2 value of 5. COL6A1, MMP3, BGN, COL1A2, and FBN2 are hub genes implicated in PDL development. Conclusion The study identified key hub genes, including COL6A1, MMP3, BGN, and FBN2, crucial for PDL formation, tissue remodeling, and cell-matrix interactions, guiding future therapeutic strategies.

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Section: Introductionmentioning

confidence: 99%

Weighted Gene Co-expression Network Analysis (WGCNA) of Wnt Signaling Related to Periodontal Ligament Formation: A Bioinformatics-Based Analysis

Yadalam,

Ramadoss,

Arumuganainar

2024

Cureus

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Dual‐Fuel Propelled Nanomotors with Two‐Stage Permeation for Deep Bacterial Infection in the Treatment of Pulpitis

Wang,

Chen,

Zhang

et al. 2023

Advanced Science

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Bacterial infection‐induced inflammatory response could cause irreversible death of pulp tissue in the absence of timely and effective therapy. Given that, the narrow structure of root canal limits the therapeutic effects of passive diffusion‐drugs, considerable attention has been drawn to the development of nanomotors, which have high tissue penetration abilities but generally face the problem of insufficient fuel concentration. To address this drawback, dual‐fuel propelled nanomotors (DPNMs) by encapsulating L‐arginine (L‐Arg), calcium peroxide (CaO2) in metal‐organic framework is developed. Under pathological environment, L‐Arg could release nitric oxide (NO) by reacting with reactive oxygen species (ROS) to provide the driving force for movement. Remarkably, the depleted ROS could be supplemented through the reaction between CaO2 with acids abundant in the inflammatory microenvironment. Owing to high diffusivity, NO achieves further tissue penetration based on the first‐stage propulsion of nanomotors, thereby removing deep‐seated bacterial infection. Results indicate that the nanomotors effectively eliminate bacterial infection based on antibacterial activity of NO, thereby blocking inflammatory response and oxidative damage, forming reparative dentine layer to avoid further exposure and infection. Thus, this work provides a propagable strategy to overcome fuel shortage and facilitates the therapy of deep lesions.

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Investigation of chromatin remodeling-related biomarkers and associated molecular mechanism in pulpitis

Li,

Sun

2025

Gene

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Identification of key module and hub genes in pulpitis using weighted gene co-expression network analysis

Cited by 4 publications

References 45 publications

Weighted Gene Co-expression Network Analysis (WGCNA) of Wnt Signaling Related to Periodontal Ligament Formation: A Bioinformatics-Based Analysis

Weighted Gene Co-expression Network Analysis (WGCNA) of Wnt Signaling Related to Periodontal Ligament Formation: A Bioinformatics-Based Analysis

Dual‐Fuel Propelled Nanomotors with Two‐Stage Permeation for Deep Bacterial Infection in the Treatment of Pulpitis

Investigation of chromatin remodeling-related biomarkers and associated molecular mechanism in pulpitis

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