Bioinformatics analyses combined microarray identify the deregulated microRNAs in oral cancer.

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The aim of the present study was to identify differentially expressed miRNAs (DE-miRNAs), which may differentiate oral cancer from normal tissues, as well as the molecular signatures that differ in tumor histology. The miRNA expression profiles of GSE28100 [the Gene Expression Omnibus (GEO) accession number] were downloaded from the GEO database and an independent sample t-test was used to identify statistical differences between the DE-miRNAs of the oral cancer patients and the healthy control subjects. The target genes of DE-miRNA were retrieved from the miRecords database. Furthermore, a protein-protein interaction network was constructed using the Search Tools for the Retrieval of Interacting Genes database and Cytoscape software. A total of 15 DE-miRNAs were identified and among them, hsa-miR-15a drew specific attention. Gene Ontology analysis revealed that the target genes of fibroblast growth factor (FGF)2 are involved in the progression of oral cancer. Furthermore, functional analysis indicated that the FGF-receptor signaling pathway was significantly upregulated in oral cancer. hsa-miR-15a is important in the regulation of oral cancer and thus, may present a potential biomarker for the prediction of oral cancer progression.", "claims": [{"id": "claim-method", "statement": "An independent sample t-test was used to identify the DE-miRNAs between the oral cancer patients and healthy control subjects, and P<0.001 was considered to indicate a statistically significant difference.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:24959249", "locator": "sections[7] \"Statistical analysis\" paragraph 2", "quote": "An independent sample t-test was used to identify the DE-miRNAs between the oral cancer patients and healthy control subjects, and P<0.001 was considered to indicate a statistically significant difference."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The miRNA expression profile of GSE28100 [the Gene Expression Omnibus (GEO) accession number] was downloaded from the GEO database, which was collected by Jung et al (8).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:24959249", "locator": "sections[3] \"Microarray analysis\" paragraph 2", "quote": "The miRNA expression profile of GSE28100 [the Gene Expression Omnibus (GEO) accession number] was downloaded from the GEO database, which was collected by Jung et al (8)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using miRNA expression profiles from GSE28100 downloaded from the GEO database and an independent-sample t-test, the study identified 15 significantly differentially expressed miRNAs (P<0.001).", "kind": "quantitative", "target": {"value": 0.001, "unit": "p-value", "tolerance": null, "source": "The miRNA expression data was analyzed by BRB-ArrayTools and 15 miRNAs exhibited significant differential expression (P<0.001; Table I)."}, "evidence": [{"asset": "source:pmid:24959249", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The miRNA expression profiles of GSE28100 [the Gene Expression Omnibus (GEO) accession number] were downloaded from the GEO database and an independent sample t-test was used to identify statistical differences between the DE-miRNAs of the oral cancer patients and the healthy control subjects."}, {"asset": "source:pmid:24959249", "locator": "sections[9] \"Identification of DE-miRNAs\" paragraph 2", "quote": "The miRNA expression data was analyzed by BRB-ArrayTools and 15 miRNAs exhibited significant differential expression (P<0.001; Table I)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using miRNA expression profiles from GSE28100 downloaded from the GEO database and an independent-sample t-test, the study identified 15 significantly differentially expressed miRNAs (P<0.001).", "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:24959249"], "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": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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