Screening and identification of key biomarkers in nasopharyngeal carcinoma: Evidence from bioinformatic analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31770211", "kind": "science-record", "revision": 4, "content_hash": "sha256:c065c21f87652430134d9b00eb01290676c26c4f692f789e9dd352a45f396c54", "created_at": "2026-11-01T17:33:12Z", "updated_at": "2026-11-01T22:01:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening and identification of key biomarkers in nasopharyngeal carcinoma: Evidence from bioinformatic analysis.", "doi": "10.1097/MD.0000000000017997", "pmid": "31770211", "authors": ["Ji-Zhou Zhang", "Zeng-Hong Wu", "Qing Cheng"], "journal": "Medicine", "year": 2019, "abstract": "As for the lack of simple and effective diagnostic methods at the early of the nasopharyngeal carcinoma (NPC), the mortality rate of NPC still remains high. Therefore, it is meaningful to explore the precise molecular mechanisms involved in the proliferation, carcinogenesis, and recurrence of NPC and thus find an effective diagnostic way and make a better therapeutic strategy.Three gene expression data sets (GSE64634, GSE53819, and GSE12452) were downloaded from Gene Expression Omnibus (GEO) and analyzed using the online tool GEO2R to identify differentially expressed genes (DEGs). Gene ontology functional analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of the DEGs were performed in Database for Annotation, Visualization and Integrated Discovery. The Search Tool for the Retrieval of Interacting Genes database was used to evaluate the interactions of DEGs and to construct a protein-protein interaction network using Cytoscape software. Hub genes were validated with the cBioPortal database.The overlap among the 3 data sets contained 306 genes were identified to be differentially expressed between NPC and non-NPC samples. A total of 13 genes (DNAAF1, PARPBP, TTC18, GSTA3, RCN1, MUC5AC, POU2AF1, FAM83B, SLC22A16, SPEF2, ERICH3, CCDC81, and IL33) were identified as hub genes with degrees ≥10.The present study was attempted to identify and functionally analyze the DEGs that may be involved in the carcinogenesis or progression of NPC by using comprehensive bioinformatics analyses and unveiled a series of hub genes and pathways. A total of 306 DEGs and 13 hub genes were identified and may be regarded as diagnostic biomarkers for NPC. However, more experimental studies are needed to carried out elucidate the biologic function of these genes results for NPC.", "claims": [{"id": "claim-method", "statement": "The identification of DEGs between NPC and noncancerous samples was performed using GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r). To correct the discovery of statistically significant genes and limitations of false-positives, we using the adjusted P-value and Benjamini and Hochberg false discovery rate method. A |log2FC| > 2 and P-value < .01 were used as considered statistically significant.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31770211", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "The identification of DEGs between NPC and noncancerous samples was performed using GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r)."}, {"asset": "source:pmid:31770211", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "To correct the discovery of statistically significant genes and limitations of false-positives, we using the adjusted P-value and Benjamini and Hochberg false discovery rate method."}, {"asset": "source:pmid:31770211", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "A |log2FC| > 2 and P-value < .01 were used as considered statistically significant."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Three gene expression data sets (GSE64634, GSE53819, and GSE12452) were downloaded from Gene Expression Omnibus (GEO) and analyzed using the online tool GEO2R to identify differentially expressed genes (DEGs).\nObserving the download of GSE64634 database included 14 NPC samples and 4 normal samples, GSE53819 data set contained 18 NPC tissue samples and 18 noncancerous samples, GSE12452 contained 31 NPC samples and 10 noncancerous samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31770211", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Three gene expression data sets (GSE64634, GSE53819, and GSE12452) were downloaded from Gene Expression Omnibus (GEO) and analyzed using the online tool GEO2R to identify differentially expressed genes (DEGs)."}, {"asset": "source:pmid:31770211", "locator": "sections[3] \"Data resources\" paragraph 2", "quote": "Observing the download of GSE64634 database included 14 NPC samples and 4 normal samples, GSE53819 data set contained 18 NPC tissue samples and 18 noncancerous samples, GSE12452 contained 31 NPC samples and 10 noncancerous samples."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using GEO2R on three GEO gene-expression datasets, the study identified 306 overlapping differentially expressed genes between NPC and non-NPC samples.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:31770211", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Three gene expression data sets (GSE64634, GSE53819, and GSE12452) were downloaded from Gene Expression Omnibus (GEO) and analyzed using the online tool GEO2R to identify differentially expressed genes (DEGs)."}, {"asset": "source:pmid:31770211", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The overlap among the 3 data sets contained 306 genes were identified to be differentially expressed between NPC and non-NPC samples."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using GEO2R on three GEO gene-expression datasets, the study identified 306 overlapping differentially expressed genes between NPC and non-NPC samples.", "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:31770211"], "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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