Gene expression profiling and bioinformatics analysis of hereditary gingival fibromatosis.

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Owing to high genetic heterogeneity, genetic testing to confirm diagnosis is not justified. It is therefore important to identify key signature genes and to understand the molecular mechanisms underlying HGF. The aim of the present study was to determine HGF-related genes and to analyze these genes through bioinformatics methods. A total of 249 differentially expressed genes (DEGs), consisting of 65 upregulated and 184 downregulated genes, were identified in the GSE4250 dataset of Gene Expression Omnibus (GEO) when comparing with the gums of HGF patients with those of healthy controls using the affy and limma packages in R. Subsequently, 28 enriched gene ontology terms were obtained from the Database for Annotation, Visualization and Integrated Discovery, and a protein-protein interaction (PPI) network was constructed and analyzed using STRING and Cytoscape. There were 99 nodes and 118 edges in the PPI network of these DEGs obtained through STRING. Among these nodes, 12 core genes were identified, of which the highest degree node was the gene for POTE ankyrin domain family member I. Collectively the results indicate that bioinformatics methods may provide effective strategies for predicting HGF-related genes and for understanding the molecular mechanisms of HGF.", "claims": [{"id": "claim-target-result", "statement": "Using the affy and limma packages in R, the study identified 249 differentially expressed genes by comparing HGF patient gingiva with healthy-control gingiva from GEO dataset GSE4250.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29435271", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 249 differentially expressed genes (DEGs), consisting of 65 upregulated and 184 downregulated genes, were identified in the GSE4250 dataset of Gene Expression Omnibus (GEO) when comparing with the gums of HGF patients with those of healthy controls using the affy and limma packages in R."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Using the affy and limma packages in R, the study identified 249 differentially expressed genes by comparing HGF patient gingiva with healthy-control gingiva from GEO dataset GSE4250.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:29435271"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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