Integrated Bioinformatics Analysis of mRNAs and miRNAs Identified Potential Biomarkers of Oral Squamous Cell Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32597160", "kind": "science-record", "revision": 8, "content_hash": "sha256:756cb9cece4483ad6d622fe6ba0a5872a2d9c3ad3185c0470809a08b18a20635", "created_at": "2026-11-01T15:41:04Z", "updated_at": "2026-11-01T22:01:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated Bioinformatics Analysis of mRNAs and miRNAs Identified Potential Biomarkers of Oral Squamous Cell Carcinoma.", "doi": "10.31557/APJCP.2020.21.6.1841", "pmid": "32597160", "authors": ["Nasrin Amiri-Dashatan", "Mehdi Koushki", "Ali Jalilian", "Nayeb Ali Ahmadi", "Mostafa Rezaei-Tavirani"], "journal": "Asian Pacific journal of cancer prevention : APJCP", "year": 2020, "abstract": "Background: Oral cancer is a frequently encountered neoplasm of the head and neck region, being the eighth most common type of human malignancy worldwide. Despite improvement in its control, morbidity and mortality, rates have improved little in the past decades. The present investigations about gene interaction and pathways still could not clear the appearance and development of oral squamous cell carcinoma (OSCC), completely. The aim of this study is to investigate the key genes and microRNAs interaction in OSCC. Materials and Methods: The microarray datasets GSE13601 and GSE98463, including mRNA and miRNA profiles, were extracted from the GEO database and were analyzed using GEO2R. Functional and pathway enrichment analyses were performed by using the DAVID database. The protein-protein interaction (PPI) network was constructed and analyzed using STRING database and Cytoscape software, respectively. Finally, miRDB was applied to predict the targets of the differentially expressed miRNAs (DEMs). Results: Totally, 97 differentially expressed genes (DEGs) were found in OSCC, including 66 up-regulated and 31 down-regulated genes. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses showed that up-regulated genes were significantly enriched in movement of cell or subcellular component, cell adhesion, biological adhesion, cellular localization, apoptotic signaling pathway, while the downregulated genes were enriched in muscle system process and oxidation-reduction process. From the PPI network, the top 10 nodes with the highest degree were detected as hub genes. In addition, 18 DEMs were screened, which included 7 up-regulated and 11 down-regulated miRNAs. STAT1 was potentially targeted by three miRNAs, including has-miR- 6825-5P, has-miR-4495, and has-miR-5580-3P. Conclusion: The roles of DEMs such as hsa-mir-5580-3p in OSCC through interactions with DEGs CD44, ACLY, ACTR3, STAT1, LAMC2 and YWHAZ may offer a suitable candidate biomarker pattern for diagnosis, prognosis and treatment processes in OSCC.", "claims": [{"id": "claim-data-access", "statement": "Above all, the differentially expressed mRNAs between patients with oral squamous cell carcinoma (OSCC) tissue (n=31) and in those with normal tongue tissue (n=26) were identified by GEO2R from the GSE13601 microarray.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32597160", "locator": "sections[2] \"Materials and Methods\" paragraph 3", "quote": "Above all, the differentially expressed mRNAs between patients with oral squamous cell carcinoma (OSCC) tissue (n=31) and in those with normal tongue tissue (n=26) were identified by GEO2R from the GSE13601 microarray."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:32597160"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE13601"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE13601"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32597160", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.31557/APJCP.2020.21.6.1841", "sha256": "sha256:bd218e0c111650865e1f16ea9d067d4755ea58848fd12d950a03527197edf145", "bytes": 29074, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.31557/APJCP.2020.21.6.1841", "version": null, "note": "Full article fetched from PMC; 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(Chamorro-Petronacci et al., 2018a)"]], "row_count": 3, "column_count": 5, "numeric_cells": 8, "header_rows": 1, "locator": "section[2]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:32597160:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bc54c8af22976cdb01b62bf6326f5e613eca3b310e5af25beb5a5bbf11d97381", "bytes": 2926, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#T2", "version": null, "note": "Functional and Pathway Enrichment Analysis of Up-Regulated and Down-Regulated Genes in Oral Squamous Cell Carcinoma (OSCC) Tissue", "structure": {"pmcid": "PMC7568896", "section_index": 3, "section_title": "Results", "row_count": 39, "column_count": 4}, "table": {"label": "Table 2", "caption": "Functional and Pathway Enrichment Analysis of Up-Regulated and Down-Regulated Genes in Oral Squamous Cell Carcinoma (OSCC) Tissue", "rows": 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"has-miR-6825-5P, has-miR-1290, miR-5580-3P"], ["YWHAQ", "6", "has-miR-6825-5P, has-miR-509-3-5P"], ["HIF1A", "6", "has-miR-4495, has-miR-509-3-5P"]], "row_count": 11, "column_count": 3, "numeric_cells": 22, "header_rows": 1, "locator": "section[3]/table-wrap[2]#T3"}}, {"id": "asset:table:pmid:32597160:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8dc4cd5eff7f682202f156535f50d99b458ac04c78b9ed8db12926797cbbef23", "bytes": 723, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[3]#T4", "version": null, "note": "Functional (Biological Process) Enrichment Analysis of the Genes in the Module", "structure": {"pmcid": "PMC7568896", "section_index": 3, "section_title": "Results", "row_count": 7, "column_count": 4}, "table": {"label": "Table 4", "caption": "Functional (Biological Process) Enrichment Analysis of the Genes in the Module", "rows": [["Category", "Term", "Count", "P-value"], ["GOTERM_BP_FAT", "GO:0044085~cellular component biogenesis", "7", "9.70E-03"], ["GOTERM_BP_FAT", "GO:0002070~epithelial cell maturation", "2", "1.50E-02"], ["GOTERM_BP_FAT", "GO:0051130~positive regulation of cellular component organization", "", "1.50E-02"], ["GOTERM_BP_FAT", "GO:0045926~negative regulation of growth", "5", "1.50E-02"], ["GOTERM_BP_FAT", "GO:0010941~regulation of cell death", "3", "2.60E-02"], ["GOTERM_BP_FAT", "GO:0006915~apoptotic process", "5", "3.20E-02"]], "row_count": 7, "column_count": 4, "numeric_cells": 17, "header_rows": 1, "locator": "section[3]/table-wrap[3]#T4"}}, {"id": "asset:table:pmid:32597160:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:aa3754f4cd86f27fdc571e8d587bd9f055953e0f842a92fb85beed482b08b361", "bytes": 1234, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[4]#T5", "version": null, "note": "Significantly DEMs in OSCC Tissue and Their Potential Target Genes", "structure": {"pmcid": "PMC7568896", "section_index": 3, "section_title": "Results", "row_count": 11, "column_count": 3}, "table": {"label": "Table 5", "caption": "Significantly DEMs in OSCC Tissue and Their Potential Target Genes", "rows": [["miRNAs", "logFC", "Target Genes"], ["has-miR-let-7d-3p", "0.79", "PARP11, HMGA2, SH3RF1, MEX3C, SEC24D, BEND2, PTGIS, PRKACB, GSTK1, PHF14"], ["has-miR-6825-5p", "0.93", "NACC1, ENO1, BACH2, RIMS3, VAT1, STAT1, BCAS1, CDK18, YWHAZ, YEHAQ"], ["has-miR-7111-5p", "1.01", "PPP1R9B, CD44, WIZ, SLC6A17, NFIX, NR1D1, ACLY, ELK1, SRF, CASTOR2"], ["has-miR-4495", "1.15", "MYH11, PIAS2, HIF1A, TMEM33, EXTL2, STAT1, PIEZO2, AZIN1, GPR173, IKZF2"], ["has-miR-1290", "1.36", "SGO1, ACTR3, RTKN2, OSBPL6, ACER3, MYH11, AKAP2, YWHAZ-AKAP2, GTF2I"], ["has-miR-509-3-5P", "-1.26", "CALD1, SERTAD2, AGFG1, ACLY, HIF1A, YWHAQ, 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