Research Article


DOI :10.26650/eor.20241393951   IUP :10.26650/eor.20241393951    Full Text (PDF)

In silico prediction of differentially expressed genes and functionally grouped networks in patients with inflamed pulp for screening pulpitis biomarkers

Azizeh AsadzadehFatemeh Shams MoattarAzam Moshfegh

Purpose: Pulpitis is one of the most common oral inflammatory diseases. There are many limitations in the traditional methods of diagnosing pulpitis. By replacing new diagnostic ways based on biomarkers, it is possible to quickly and accurately identify this disease. Biological indicators have greatly helped not only in the screening of infectious diseases but also in early and appropriate treatment. In this research, differentially expressed genes (DEGs) related to pulpitis were analyzed, and prognostic biomarkers were introduced.

Materials and methods: In this in silico study, we applied the GSE77459 dataset as the gene expression profile of pulpitis. Web tool, GEO2R was used to separate up-regulated and down-regulated DEGs. |logFC|>2 and adjusted p-value < 0.05 was set as the cut-off criterion. For the pathway enrichment study of obtained genes, EnrichR was implemented. After constructing a protein‑protein interaction (PPI) network, hub genes that are involved in pulpitis were selected. Finally, functionally grouped networks by ClueGO software (v2.5.10) were generated.

Results: GEO2R analysis of the GSE77459 dataset showed 672 up-regulated genes and 239 down-regulated genes with GB_ACC code. Based on Cytoscape results, the 15 top hubba nodes were ranked including PTPRC, ITGAM, CCL2, ICAM1, MMP9, CXCL8, TLR2, CD86, CXCR4, IL1A, CD44, CCL3, ITGAX, CXCL10, and CCR7. Functionally grouped networks determined that these genes were mainly enriched in chemokine-mediated signaling pathway, morphogenesis of endothelium, and neuroinflammatory response.

Conclusion: In our research, 15 genes were introduced as diagnostic biomarkers in pulpitis and their functionally grouped networks were constructed. However, the obtained results need to be validated using in vitro and in vivo methods.


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APA

Asadzadeh, A., Moattar, F.S., & Moshfegh, A. (2024). In silico prediction of differentially expressed genes and functionally grouped networks in patients with inflamed pulp for screening pulpitis biomarkers. European Oral Research, 0(0), -. https://doi.org/10.26650/eor.20241393951


AMA

Asadzadeh A, Moattar F S, Moshfegh A. In silico prediction of differentially expressed genes and functionally grouped networks in patients with inflamed pulp for screening pulpitis biomarkers. European Oral Research. 2024;0(0):-. https://doi.org/10.26650/eor.20241393951


ABNT

Asadzadeh, A.; Moattar, F.S.; Moshfegh, A. In silico prediction of differentially expressed genes and functionally grouped networks in patients with inflamed pulp for screening pulpitis biomarkers. European Oral Research, [Publisher Location], v. 0, n. 0, p. -, 2024.


Chicago: Author-Date Style

Asadzadeh, Azizeh, and Fatemeh Shams Moattar and Azam Moshfegh. 2024. “In silico prediction of differentially expressed genes and functionally grouped networks in patients with inflamed pulp for screening pulpitis biomarkers.” European Oral Research 0, no. 0: -. https://doi.org/10.26650/eor.20241393951


Chicago: Humanities Style

Asadzadeh, Azizeh, and Fatemeh Shams Moattar and Azam Moshfegh. In silico prediction of differentially expressed genes and functionally grouped networks in patients with inflamed pulp for screening pulpitis biomarkers.” European Oral Research 0, no. 0 (Nov. 2024): -. https://doi.org/10.26650/eor.20241393951


Harvard: Australian Style

Asadzadeh, A & Moattar, FS & Moshfegh, A 2024, 'In silico prediction of differentially expressed genes and functionally grouped networks in patients with inflamed pulp for screening pulpitis biomarkers', European Oral Research, vol. 0, no. 0, pp. -, viewed 22 Nov. 2024, https://doi.org/10.26650/eor.20241393951


Harvard: Author-Date Style

Asadzadeh, A. and Moattar, F.S. and Moshfegh, A. (2024) ‘In silico prediction of differentially expressed genes and functionally grouped networks in patients with inflamed pulp for screening pulpitis biomarkers’, European Oral Research, 0(0), pp. -. https://doi.org/10.26650/eor.20241393951 (22 Nov. 2024).


MLA

Asadzadeh, Azizeh, and Fatemeh Shams Moattar and Azam Moshfegh. In silico prediction of differentially expressed genes and functionally grouped networks in patients with inflamed pulp for screening pulpitis biomarkers.” European Oral Research, vol. 0, no. 0, 2024, pp. -. [Database Container], https://doi.org/10.26650/eor.20241393951


Vancouver

Asadzadeh A, Moattar FS, Moshfegh A. In silico prediction of differentially expressed genes and functionally grouped networks in patients with inflamed pulp for screening pulpitis biomarkers. European Oral Research [Internet]. 22 Nov. 2024 [cited 22 Nov. 2024];0(0):-. Available from: https://doi.org/10.26650/eor.20241393951 doi: 10.26650/eor.20241393951


ISNAD

Asadzadeh, Azizeh - Moattar, FatemehShams - Moshfegh, Azam. In silico prediction of differentially expressed genes and functionally grouped networks in patients with inflamed pulp for screening pulpitis biomarkers”. European Oral Research 0/0 (Nov. 2024): -. https://doi.org/10.26650/eor.20241393951



TIMELINE


Submitted22.11.2023
Accepted27.12.2023
Published Online13.03.2024

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