Identification of Key Genes in Nasopharyngeal Carcinoma Based on Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35712071", "kind": "science-record", "revision": 4, "content_hash": "sha256:7f9d84977a0981fb68a9c040c9297f5941386bc417a429f915c4ebc4cbfbdb20", "created_at": "2026-11-01T18:14:41Z", "updated_at": "2026-11-01T22:06:47Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Key Genes in Nasopharyngeal Carcinoma Based on Bioinformatics Analysis.", "doi": "10.1155/2022/9022700", "pmid": "35712071", "authors": ["Yujie Song", "Tao Feng", "Wenping Cao", "Haiyang Yu", "Zeng Zhang"], "journal": "Computational intelligence and neuroscience", "year": 2022, "abstract": "Objective: This study aimed to identify key genes associated with the pathogenesis of nasopharyngeal carcinoma (NPC) by bioinformatics analysis.\nMethods: Datasets (GSE13597 and GSE34573) were screened and downloaded from the comprehensive gene expression database (GEO). GEO2R online tool was adopted to analyze microarray data GSE13597 and GSE34573 related to NPC. Volcano plot was generated using Bioconductor in R software. \"Pheatmap\" was used to draw heatmaps based on the top 10 regulated genes of GSE13597 and GSE34573. GO and KEGG analyses were conducted via online tool DAVID. We uploaded the DEGs of NPC to STRING software and then used Cytoscape software to draw PPI network of DEGs.\nResults: 216 DEGs were obtained in GSE13597 between patient and control group (111 up-regulated DEGs and 105 down-regulated DEGs). 1101 DEGs were obtained in GSE34573 (470 up-regulated DEGs and 641 down-regulated DEGs). 63 common differential genes were screened named co-DEGs in the two datasets. These DEGs were mainly associated with defense response to bacterium, cell-matrix adhesion, chemokine-mediated signaling pathway, tissue homeostasis, humoral immune response, cilium movement, cilium organization, cilium assembly, and epithelial cilium movement. KEGG pathway enrichment analysis showed that DEGs were mainly involved in viral protein interaction with cytokine and cytokine receptor, salivary secretion, p53 signaling pathway, IL-17 signaling pathway, cell cycle, PI3K-Akt signaling pathway, and ECM-receptor interaction. We identified seven hub genes, including FN1, MMP-10, MUC1, KIF23, CDK1, MUC5B, and MUC5AC.\nConclusions: Seven hub genes, including FN1, MMP-10, MUC1, KIF23, CDK1, MUC5B, and MUC5AC, might be therapeutic potential biomarkers of NPC.", "claims": [{"id": "claim-method", "statement": "Firstly, we used GEO2R tool to analyze microarray data GSE13597 and GSE34573 related to nasopharyngeal carcinoma.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35712071", "locator": "sections[4] \"2.2. Identification of DEGs\" paragraph 2", "quote": "Firstly, we used GEO2R tool to analyze microarray data GSE13597 and GSE34573 related to nasopharyngeal carcinoma."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data used to support the findings of this study are available on reasonable request from the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35712071", "locator": "sections[12] \"Data Availability\" paragraph 2", "quote": "Data used to support the findings of this study are available on reasonable request from the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "GSE13597 and GSE34573 were analyzed online by GEO2R. 216 DEGs were obtained in GSE13597 between patient and control group (111 up-regulated DEGs and 105 down-regulated DEGs) (Figure 1(a)). 1101 DEGs were obtained in GSE34573 (470 up-regulated DEGs and 641 down-regulated DEGs) (Figure 1(b)).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35712071", "locator": "sections[8] \"3.1. Identification of DEGs\" paragraph 2", "quote": "GSE13597 and GSE34573 were analyzed online by GEO2R. 216 DEGs were obtained in GSE13597 between patient and control group (111 up-regulated DEGs and 105 down-regulated DEGs) (Figure 1(a)). 1101 DEGs were obtained in GSE34573 (470 up-regulated DEGs and 641 down-regulated DEGs) (Figure 1(b))."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "GSE13597 and GSE34573 were analyzed online by GEO2R. 216 DEGs were obtained in GSE13597 between patient and control group (111 up-regulated DEGs and 105 down-regulated DEGs) (Figure 1(a)). 1101 DEGs were obtained in GSE34573 (470 up-regulated DEGs and 641 down-regulated DEGs) (Figure 1(b)).", "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:35712071"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35712071", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/9022700", "sha256": "sha256:005b8b474096ec84e2a9d244a53aefa215b090ba499c32d77660492b7ce9d0fb", "bytes": 14232, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/9022700", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9197650", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "PPI"}}, {"id": "method-2", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}, {"id": "method-3", "family": null, "specific": null, "label": "GEO2R", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Firstly, we used GEO2R tool to analyze microarray data GSE13597 and GSE34573 related to nasopharyngeal carcinoma."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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