Analyzing Pooled Microarray Gene Expression Data to Uncover Common Pathways in Periodontitis and Oral Squamous Cell Carcinoma from the Gene Expression Omnibus.

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Gene expression datasets from the gene expression omnibus (GEO) repository (GSE30784 for OSCC and GSE10334 for periodontitis) were analyzed. Data preprocessing and differential gene expression analysis using GEO2R identified common differentially expressed genes (DEGs), and FunRich software facilitated the construction of a protein-protein interaction (PPI) network on the STRING database. Cytoscape, coupled with the CytoHubba plugin, identified Cluster of Differentiation 19 (CD19) and Von Willebrand Factor (VWF) as the top hub genes, with Complement C3 (C3) also highly ranked. Functional enrichment analysis highlighted pathways such as the B-cell receptor signaling pathway, complement and coagulation cascades, and hematopoietic cell lineage. Additionally, miRNet analysis identified key miRNAs, including hsa-mir-26a-5p, hsa-mir-129-2-3p, and hsa-mir-27a-3p, associated with these pathways. These findings suggested an association of molecular mechanisms between periodontitis and OSCC, with identified hub genes and miRNAs potentially serving as therapeutic targets.", "claims": [{"id": "claim-method", "statement": "The R packages GEO query and limma were used to generate a text file listing DEGs with log fold change (logFC) values, P values, adjusted P values, gene symbols, gene IDs, and gene names—genes with a P value ≤ 0.05 and a logFC ≥ 0.5 were included as DEGs for both diseases.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38882729", "locator": "sections[4] \"Data processing and differentially expressed genes (DEGs)\" paragraph 2", "quote": "The R packages GEO query and limma were used to generate a text file listing DEGs with log fold change (logFC) values, P values, adjusted P values, gene symbols, gene IDs, and gene names—genes with a P value ≤ 0.05 and a logFC ≥ 0.5 were included as DEGs for both diseases."}], "state": "complete"}, {"id": "claim-target-result", "statement": "These findings suggested an association of molecular mechanisms between periodontitis and OSCC, with identified hub genes and miRNAs potentially serving as therapeutic targets.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38882729", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "These findings suggested an association of molecular mechanisms between periodontitis and OSCC, with identified hub genes and miRNAs potentially serving as therapeutic targets."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "These findings suggested an association of molecular mechanisms between periodontitis and OSCC, with identified hub genes and miRNAs potentially serving as therapeutic targets.", "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:38882729"], "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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