Introducing Critical Pain Related Genes: A System Biology Approach

Tavirani, Mostafa Rezaei; Tavirani, Sina Rezaei; Zadeh-Esmaeel, Mohammad-Mahdi; Ahmadi, Nayeb Ali

doi:10.32598/bcn.9.10.310

Cited by 2 publications

(2 citation statements)

References 25 publications

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“…Several omics-based investigations were performed on differentially expressed genes (DEGs) in painful diabetic peripheral neuropathy models to identify DEGs contributing to pathological processes and neuropathic pain (14)(15)(16). Additionally, network-based analysis can explain the critical genes associated with different diseases (13,17,18). Since the full mechanism of painful diabetic neuropathy is not clear, the protein interaction network analysis could be a promising way to manage this problem.…”

Section: Introductionmentioning

confidence: 99%

Introducing Pain-Related Molecular Pathways in Painful Diabetic Neuropathy Via Protein Interaction Networks

Amiri-Dashatan,

Farrokhi-Yekta,

Koushki

et al. 2024

J Cell Mol Anesth

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Background: Painful diabetic neuropathy (PDN) is one of the most drastic complications of diabetes. Patients with PDN always reveal spontaneous and stimulus‑evoked pain. However, the pathogenesis mechanisms of PDN are not entirely distinct. Objectives: In the present study protein-protein interaction (PPI) network for PDN was constructed and analyzed to identify key proteins as potential biomarker candidates. Methods: The transcriptomic (genes) and proteomic (proteins) data in articles that focused on PDN with differential expressions were collected. Protein networks were constructed and analyzed using STRING and Cytoscape software, respectively. Further PPI network analysis, gene ontology, and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis were performed using MCODE and DAVID tools. Results: A total of 147 differentially regulated proteins/genes were identified in painful diabetic neuropathy, including 91 up-regulated and 56 down-regulated proteins/genes. A network analysis of genes/proteins related to PDN identified COX4I1, NDUFS8, UQCRC1, COX7C, and some other NADH dehydrogenases, including NDUFB7, NDUFS7, NDUFS3, NDUFB5, NDUFA2, and NDUFB4 as hub-bottleneck proteins. With functional enrichment analysis of network clustering, COX7C, HP, RPS12, KCNIP2, and CoL4A1 were established as distinct seed proteins in the obtained modules, which could lead to the discovery of biomarker candidates. Conclusions: These results could provide new insights into pathology and molecular mechanisms, as well as the identification of pathways and proteins/genes involved in causing PDN in diabetic patients. COX7C, HP, RPS12, KCNIP2, and CoL4A1 are the top 5 seed nodes (hub proteins) and can serve as potential biomarker candidates and targets for PDN management. However, further investigations are needed to evaluate these proteins in detail.

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Section: Introductionmentioning

confidence: 99%

Introducing Pain-Related Molecular Pathways in Painful Diabetic Neuropathy Via Protein Interaction Networks

Amiri-Dashatan,

Farrokhi-Yekta,

Koushki

et al. 2024

J Cell Mol Anesth

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“…Alterations in their expression could cause differentiation in the system of interactions. 11 Consequently, in this study, proteins with differential expression in the treatment with proton are investigated more in terms of interaction properties to introduce the potential ones.…”

Section: Introductionmentioning

confidence: 99%

The Highlighted Role of GAPDH and Nitric-Oxide Synthase Regulator Activity in Proton Beam Irradiated Melanoma BLM Cells

et al. 2019

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Introduction: The human melanoma is a type of invasive tumor the treatment of which is challenging. To better understand the proton irradiation mechanisms as one of the widely applied therapy for this type of cancer, bioinformatics analysis of proteomics outcome could be beneficial. Methods: Protein-protein interaction network analysis of the differentially expressed proteins (DEPs) of melanoma BLM (BRO lung metastasis) cells in the treatment of 3 Gy dosage proton therapy was performed in this study via Cytoscape V.3.7.2. and its integrated plug-ins. Results: Eighteen DEPs were searched for network constructions and limited numbers of query +neighbor proteins were found central. The hub-bottlenecks (i.e. central nodes) were GAPDH, ACTB, ALB, AKT1, TP53, and EGFR. The fist mentioned proteins were from DEPs. The enrichment analysis of these elements identified nitric-oxide synthase regulator activity and the positive regulation of the norepinephrine uptake that may be the key to the mechanisms of proton therapy. Conclusion: In conclusion, the identified central nodes (EGFR, TP53, ALB, AKT1, GAPDH, and ACTB) and the related biological terms are the critical affected genes and biological terms in the irradiated melanoma cells.

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Introducing Critical Pain Related Genes: A System Biology Approach

Cited by 2 publications

References 25 publications

Introducing Pain-Related Molecular Pathways in Painful Diabetic Neuropathy Via Protein Interaction Networks

Introducing Pain-Related Molecular Pathways in Painful Diabetic Neuropathy Via Protein Interaction Networks

The Highlighted Role of GAPDH and Nitric-Oxide Synthase Regulator Activity in Proton Beam Irradiated Melanoma BLM Cells

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