Identifying key genes and small molecule compounds for nasopharyngeal carcinoma by various bioinformatic analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34664875", "kind": "science-record", "revision": 5, "content_hash": "sha256:7632784cbabff0581d219b51a8f97c7f28f8e813165db4a358c3126bb3d3e450", "created_at": "2026-11-01T17:36:20Z", "updated_at": "2026-11-01T22:47:44Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identifying key genes and small molecule compounds for nasopharyngeal carcinoma by various bioinformatic analysis.", "doi": "10.1097/MD.0000000000027257", "pmid": "34664875", "authors": ["Lucheng Fang", "Licai Shi", "Wen Wang", "Qinjuan Chen", "Xingwang Rao"], "journal": "Medicine", "year": 2021, "abstract": "ABSTRACT: Nasopharyngeal carcinoma (NPC) is one of the most prevalent head and neck cancer in southeast Asia. It is necessary to proceed further studies on the mechanism of occurrence and development of NPC.In this study, we employed the microarray dataset GSE12452 and GSE53819 including 28 normal samples and 49 nasopharyngeal carcinoma samples downloaded from the Gene Expression Omnibus(GEO) to analysis. R software, STRING, CMap, and various databases were used to screen differentially expressed genes (DEGs), construct the protein-protein interaction (PPI) network, and proceed small molecule compounds analysis, among others.Totally, 424 DEGs were selected from the dataset. DEGs were mainly enriched in extracellular matrix organization, cilium organization, PI3K-Akt signaling pathway, collagen-containing extracellular matrix, and extracellular matrix-receptor interaction, among others. Top 10 upregulated and top 10 downregulated hub genes were identified as hub DEGs. Piperlongumine, apigenin, menadione, 1,4-chrysenequinone, and chrysin were identified as potential drugs to prevent and treat NPC. Besides, the effect of genes CDK1, CDC45, RSPH4A, and ZMYND10 on survival of NPC was validated in GEPIA database.The data revealed novel aberrantly expressed genes and pathways in NPC by bioinformatics analysis, potentially providing novel insights for the molecular mechanisms governing NPC progression. Although further studies needed, the results demonstrated that the expression levels of CDK1, CDC45, RSPH4A, and ZMYND10 probably affected survival of NPC patients.", "claims": [{"id": "claim-method", "statement": "We identified DEGs between normal and NPC samples using the Limma software package in R.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34664875", "locator": "sections[3] \"Data resources and extraction of DEGs\" paragraph 2", "quote": "We identified DEGs between normal and NPC samples using the Limma software package in R."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analyzed during this study are included in this published article [and its supplementary information files].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34664875", "locator": "sections[17] \"fn-group\" paragraph 1", "quote": "All data generated or analyzed during this study are included in this published article [and its supplementary information files]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Totally, 424 DEGs were selected from the dataset.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34664875", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Totally, 424 DEGs were selected from the dataset."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Totally, 424 DEGs were selected from the dataset.", "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:34664875"], "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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