Identification of key biomarkers and potential therapeutic drugs in nasopharyngeal carcinoma based on comprehensive bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40591047", "kind": "science-record", "revision": 2, "content_hash": "sha256:b784af0c640ba48a40edacf7c9e54bf66e9b6b5300f5efb3a21cf34c913f6396", "created_at": "2026-11-01T20:30:40Z", "updated_at": "2026-11-01T21:35:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of key biomarkers and potential therapeutic drugs in nasopharyngeal carcinoma based on comprehensive bioinformatics analysis.", "doi": "10.1007/s12672-025-03047-4", "pmid": "40591047", "authors": ["Cong Fu", "Lin Sun", "Lili Zhang", "Tong Zhou", "Yanzhi Bi"], "journal": "Discover oncology", "year": 2025, "abstract": "Nasopharyngeal carcinoma (NPC) is the most prevalent type of head- and -neck cancer, and its diagnosis and treatment are currently facing significant challenges. This study aimed to identify biomarkers associated with NPC by performing bioinformatic analysis on the GSE12452, GSE53819, and GSE64634 datasets from the GEO database. First, differentially expressed genes (DEGs) between NPC and normal nasopharyngeal tissues were screened. Then, these DEGs were subjected to RobustRank Aggregation analysis. Through Receiver Operating Characteristic (ROC) analysis and three machine-learning models, biomarkers such as DNAH5, ZMYND10, LRRC6, ARMC4, DNAI2, and DNALI1 were identified. Enrichment analysis was performed to uncover the common pathways of these biomarkers. Using the Comparative Toxicogenomics Database (CTD), target drugs for NPC were predicted based on these biomarkers. Additionally, immune infiltration analysis was carried out to study the relationship between these biomarkers and immune cells. A regulatory network was also constructed. It was found that these biomarkers are mainly involved in cytokine-cytokine receptor interaction, and some are part of common cancer-related signaling pathways. In addition, quantitative real time polymerase chain reaction (qRT-PCR) results showed that the expression levels of all biomarkers were significantly elevated in normal cell samples. DNAH5 and ZMYND10 were significantly higher in normal surrounding tissues. These findings provided potential support for the early clinical diagnosis and treatment of nasopharyngeal carcinoma patients.", "claims": [{"id": "claim-method", "statement": "Thus, RobustRankAggreg R package (v 1.2.1) [84] was employed to integrate the DEGs from the three datasets mentioned above.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40591047", "locator": "sections[16] \"Integration of microarray data\" paragraph 2", "quote": "Thus, RobustRankAggreg R package (v 1.2.1) [84] was employed to integrate the DEGs from the three datasets mentioned above."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analysed during the current study are available in the [Gene Expression Omnibus (GEO)] repository, [https://www.ncbi.nlm.nih.gov/gds], reference number [GSE12452, GSE53819 and GSE64634].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40591047", "locator": "sections[31] \"Data availability\" paragraph 2", "quote": "The datasets analysed during the current study are available in the [Gene Expression Omnibus (GEO)] repository, [https://www.ncbi.nlm.nih.gov/gds], reference number [GSE12452, GSE53819 and GSE64634]."}], "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:40591047"], "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:GSE12452"], "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:GSE12452"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40591047", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s12672-025-03047-4", "sha256": "sha256:a6ed6931f13df8220d5b88e19436b870110f281afc3a6ade531af203b095ba01", "bytes": 63911, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s12672-025-03047-4", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12214193", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE12452", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12452", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE12452", "version": null, "note": "The datasets analysed during the current study are available in the [Gene Expression Omnibus (GEO)] repository, [https://www.ncbi.nlm.nih.gov/gds], reference number [GSE12452, GSE53819 and GSE64634].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analysed during the current study are available in the [Gene Expression Omnibus (GEO)] repository, [https://www.ncbi.nlm.nih.gov/gds], reference number [GSE12452, GSE53819 and GSE64634].", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM312896", "GSM312897", "GSM312898", "GSM312899", "GSM312900", "GSM312901", "GSM312902", "GSM312903", "GSM312904", "GSM312905", "GSM312906", "GSM312907", "GSM312908", "GSM312909", "GSM312910", "GSM312911", "GSM312912", "GSM312913", "GSM312914", "GSM312915", "GSM312916", "GSM312917", "GSM312918", "GSM312919", "GSM312920", "GSM312921", "GSM312922", "GSM312923", "GSM312924", "GSM312925", "GSM312926", "GSM312927", "GSM312928", "GSM312929", "GSM312930", "GSM312931", "GSM312932", "GSM312933", "GSM312934", "GSM312935", "GSM312936"], "sample_count": 41, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "mRNA expression profiling of nasopharyngeal carcinoma", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE53819", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53819", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE53819", "version": null, "note": "The datasets analysed during the current study are available in the [Gene Expression Omnibus (GEO)] repository, [https://www.ncbi.nlm.nih.gov/gds], reference number [GSE12452, GSE53819 and GSE64634].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analysed during the current study are available in the [Gene Expression Omnibus (GEO)] repository, [https://www.ncbi.nlm.nih.gov/gds], reference number [GSE12452, GSE53819 and GSE64634].", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1301444", "GSM1301445", "GSM1301446", "GSM1301447", "GSM1301448", "GSM1301449", "GSM1301450", "GSM1301451", "GSM1301452", "GSM1301453", "GSM1301454", "GSM1301455", "GSM1301456", "GSM1301457", "GSM1301458", "GSM1301459", "GSM1301460", "GSM1301461", "GSM1301462", "GSM1301463", "GSM1301464", "GSM1301465", "GSM1301466", "GSM1301467", "GSM1301468", "GSM1301469", "GSM1301470", "GSM1301471", "GSM1301472", "GSM1301473", "GSM1301474", "GSM1301475", "GSM1301476", "GSM1301477", "GSM1301478", "GSM1301479"], "sample_count": 36, "group_sizes": null, "group_sizes_basis": null, "platform": "6480", "taxon": "Homo sapiens", "title": "Genome-wide expressing profiling of nasopharyngeal carcinoma primary tumors versus non-cancerous nasopharyngeal tissues.", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE64634", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE64634", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE64634", "version": null, "note": "The datasets analysed during the current study are available in the [Gene Expression Omnibus (GEO)] repository, [https://www.ncbi.nlm.nih.gov/gds], reference number [GSE12452, GSE53819 and GSE64634].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analysed during the current study are available in the [Gene Expression Omnibus (GEO)] repository, [https://www.ncbi.nlm.nih.gov/gds], reference number [GSE12452, GSE53819 and GSE64634].", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1575894", "GSM1575895", "GSM1575896", "GSM1575897", "GSM1575898", "GSM1575899", "GSM1575900", "GSM1575901", "GSM1575902", "GSM1575903", "GSM1575904", "GSM1575905", "GSM1575906", "GSM1575907", "GSM1575908", "GSM1575909"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "mRNA expression profiling of nasopharyngeal carcinoma", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE12452 not downloaded", "asset:data:geo:GSE12452 licence not read", "asset:data:geo:GSE53819 not downloaded", "asset:data:geo:GSE53819 licence not read", "asset:data:geo:GSE64634 not downloaded", "asset:data:geo:GSE64634 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Robust Rank Aggregation (RRA)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Thus, RobustRankAggreg R package (v 1.2.1) [84] was employed to integrate the DEGs from the three datasets mentioned above."}}], "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": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Robust Rank Aggregation (RRA)), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE12452", "GSE53819", "GSE64634"], "resolved_accessions": ["GSE12452", "GSE53819", "GSE64634"], "statements": ["The datasets analysed during the current study are available in the [Gene Expression Omnibus (GEO)] repository, [https://www.ncbi.nlm.nih.gov/gds], reference number [GSE12452, GSE53819 and GSE64634]."], "basis": "The paper names GSE12452, GSE53819, GSE64634 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:40591047", "data:geo:GSE12452"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE12452"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:55:23Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 18100, "completion_tokens": 2718, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:40591047", "type": "paper", "label": "pmid:40591047"}, {"id": "source:pmid:40591047", "type": "manuscript", "label": "PMID 40591047 full text"}, {"id": "data:geo:GSE12452", "type": "dataset", "label": "GEO GSE12452"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40591047", "type": "paper", "label": "pmid:40591047"}, {"id": "source:pmid:40591047", "type": "manuscript", "label": "PMID 40591047 full text"}, {"id": "data:geo:GSE12452", "type": "dataset", "label": "GEO GSE12452"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40591047", "type": "extraction", "used": ["source:pmid:40591047"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE12452", "type": "accession_resolution", "used": ["data:geo:GSE12452"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:40591047", "parent_hash": "sha256:ec0c7703d97ab8ce030cc1b4946d512022a37c5867e68ce2b41973efa17199ec", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE12452 licence not read", "asset:data:geo:GSE12452 not downloaded", "asset:data:geo:GSE53819 licence not read", "asset:data:geo:GSE53819 not downloaded", "asset:data:geo:GSE64634 licence not read", "asset:data:geo:GSE64634 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["ioscience Inc, Shanghai. The cell density of cultured Primary human nasal epithelial cells (HNEC),"], "order_basis": "paper_text_order:1916", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["en conducted using Universal Blue SYBR Green qPCR Master Mix. The qRT-PCR thermocycling condit"], "order_basis": "paper_text_order:2807", "id": "assay:2"}]}