Bioinformatics, Interaction Network Analysis, and Neural Networks to Characterize Gene Expression of Radicular Cyst and Periapical Granuloma

Poswar, Fabiano de Oliveira; Farias, Lucyana Conceição; Fraga, Carlos Alberto de Carvalho; Bambirra, Wilson; Brito-Júnior, Manoel; Sousa‐Neto, Manoel Damião; Santos, Sérgio Henrique Sousa; Paula, Alfredo Maurício Batista de; D’Angelo, Marcos Flávio Silveira Vasconcelos; Guimarães, André Luiz Sena

doi:10.1016/j.joen.2015.02.004

Cited by 34 publications

(28 citation statements)

References 50 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The cluster analysis was performed on the predicted 39 genes using the K-means 28 clustering method in STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) (http://string-db.org/) to identify groups within them so as to prioritize genes for experimental validation. The analysis resulted in a network with high clustering coefficient of 0.58 and the average degree of ~13.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Identification of oral cancer related candidate genes by integrating protein-protein interactions, gene ontology, pathway analysis and immunohistochemistry

Kumar

Samal

Routray

et al. 2017

Sci Rep

View full text Add to dashboard Cite

In the recent years, bioinformatics methods have been reported with a high degree of success for candidate gene identification. In this milieu, we have used an integrated bioinformatics approach assimilating information from gene ontologies (GO), protein–protein interaction (PPI) and network analysis to predict candidate genes related to oral squamous cell carcinoma (OSCC). A total of 40973 PPIs were considered for 4704 cancer-related genes to construct human cancer gene network (HCGN). The importance of each node was measured in HCGN by ten different centrality measures. We have shown that the top ranking genes are related to a significantly higher number of diseases as compared to other genes in HCGN. A total of 39 candidate oral cancer target genes were predicted by combining top ranked genes and the genes corresponding to significantly enriched oral cancer related GO terms. Initial verification using literature and available experimental data indicated that 29 genes were related with OSCC. A detailed pathway analysis led us to propose a role for the selected candidate genes in the invasion and metastasis in OSCC. We further validated our predictions using immunohistochemistry (IHC) and found that the gene FLNA was upregulated while the genes ARRB1 and HTT were downregulated in the OSCC tissue samples.

show abstract

Section: Resultsmentioning

confidence: 99%

“…enrichment of GO, pathways, and clustering etc. In the current study, the k-means clustering as implied in STRING was used to cluster the genes 28 . The clustering was done on the basis of evidence score and connection cutoff was kept at 0.40.…”

Section: Methodsmentioning

confidence: 99%

Identification of oral cancer related candidate genes by integrating protein-protein interactions, gene ontology, pathway analysis and immunohistochemistry

Kumar

Samal

Routray

et al. 2017

Sci Rep

View full text Add to dashboard Cite

show abstract

“…The leader gene approach could be used in different contexts and for different purposes [52, 53]. In the current study, we use bioinformatics to predict the central pathways affected by metformin under hypoxia.…”

Section: Discussionmentioning

confidence: 99%

“…The leader gene approach was described previously [53, 65, 66]. Briefly, OSCC, Metformin, and Hypoxia were used as keywords together when searched in PubMed.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Metformin increases PDH and suppresses HIF-1α under hypoxic conditions and induces cell death in oral squamous cell carcinoma

et al. 2016

Self Cite

View full text Add to dashboard Cite

BackgroundMetformin is a biguanide, belonging to the oral hypoglycemic agents and is a widely used in the treatment of type 2 diabetes. Evidence indicate that Metformin inhibits cell proliferation in several human cancers and inhibits the Warburg phenomenon in tumor cells.ResultsLow PDH levels were observed in OSCC, and Metformin promotes an increase in PDH levels in hypoxic conditions. Metformin also reduced HIF-1α mRNA and protein levels. Metformin demonstrated antiproliferative effects, inhibited migration, increased the number of apoptotic cells and increased the transcription of caspase 3.ObjectiveThe present study aims to explore the effects of Metformin in hypoxic conditions. Specifically, we focused on pyruvate dehydrogenase (PDH), (hypoxia-inducible factor 1α) HIF-1α levels and the oral squamous cell carcinoma (OSCC) cell phenotype. Additionally, we also investigated a theoretical consequence of Metformin treatment.MethodsPDH levels in patients with OSCC and oral dysplasia were evaluated. Metformin was administered in vitro to test the effect of Metformin under hypoxic conditions. The results were complemented by Bioinformatics analyses.ConclusionsIn conclusion, our current findings show that Metformin reduces HIF-1α gene expression and increases PDH expression. Metformin inhibits cell proliferation and migration in the OSCC cell line model. Additionally, Metformin enhances the number of apoptotic cells and caspase 3 levels. Interestingly enough, Metformin did not increase the mutant p53 levels under hypoxic conditions.

show abstract

Etiology and Pathogenesis of Pulpitis and Apical Periodontitis

Fouad¹,

Khan²

2019

Essential Endodontology

View full text Add to dashboard Cite

Bioinformatics, Interaction Network Analysis, and Neural Networks to Characterize Gene Expression of Radicular Cyst and Periapical Granuloma

Cited by 34 publications

References 50 publications

Identification of oral cancer related candidate genes by integrating protein-protein interactions, gene ontology, pathway analysis and immunohistochemistry

Identification of oral cancer related candidate genes by integrating protein-protein interactions, gene ontology, pathway analysis and immunohistochemistry

Metformin increases PDH and suppresses HIF-1α under hypoxic conditions and induces cell death in oral squamous cell carcinoma

Etiology and Pathogenesis of Pulpitis and Apical Periodontitis

Contact Info

Product

Resources

About