Comprehensive analysis reveals novel gene signature in head and neck squamous cell carcinoma: predicting is associated with poor prognosis in patients.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35117201", "kind": "science-record", "revision": 5, "content_hash": "sha256:e468fb2406425625ceda7fea3abebfa12750166de35e04410f856ae8c409a1f6", "created_at": "2026-11-01T17:36:51Z", "updated_at": "2026-11-01T22:48:23Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive analysis reveals novel gene signature in head and neck squamous cell carcinoma: predicting is associated with poor prognosis in patients.", "doi": "10.21037/tcr-20-805", "pmid": "35117201", "authors": ["Yixin Sun", "Quan Zhang", "Lanlin Yao", "Shuai Wang", "Zhiming Zhang"], "journal": "Translational cancer research", "year": 2020, "abstract": "BACKGROUND: Head and neck squamous cell carcinoma (HNSC) remains an important public health problem, with classic risk factors being smoking and excessive alcohol consumption and usually has a poor prognosis. Therefore, it is important to explore the underlying mechanisms of tumorigenesis and screen the genes and pathways identified from such studies and their role in pathogenesis. The purpose of this study was to identify genes or signal pathways associated with the development of HNSC.\nMETHODS: In this study, we downloaded gene expression profiles of GSE53819 from the Gene Expression Omnibus (GEO) database, including 18 HNSC tissues and 18 normal tissues. The differentially expressed genes (DEGs) were identified using the Linear Models for Microarray Data R package. Adjusted P values <0.01 and |log2 fold change (FC)| ≥2 was regarded as the filter condition. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of these DEGs were performed on the Database for Annotation, Visualization, and Integrated Discovery (DAVID) online website. Protein-protein interaction (PPI) network was built to visualize the interactions between these DEGs using the STRING online website. Finally, hub genes were identified by The Cancer Genome Atlas (TCGA) database.\nRESULTS: A total of 604 DEGs consisting of 159 upregulated genes and 445 downregulated genes were selected. From these DEGs, prognostic related genes could serve as potential biomarkers for the molecular diagnosis and therapeutic intervention of HNSC were identified. Including the known genes, GPR18, CNR2, RSPH4A, ULBP2, TEX101, and STC2. And the novel genes, CCR8, CCDC39, CNTN5, MSLN, and CHGB were strongly implicated in HNSC.\nCONCLUSIONS: In summary, we indicated genes associated with prognostic in patients, which improve our understanding of HNSC and could be used as new therapeutic targets for HNSC.", "claims": [{"id": "claim-method", "statement": "We used the Benjamini and Hochberg methods, genes with |log2-fold change (FC)| ≥2 and adjusted P values <0.01 were used in the next analysis stage (11).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35117201", "locator": "sections[5] \"Identification of DEGs\" paragraph 2", "quote": "We used the Benjamini and Hochberg methods, genes with |log2-fold change (FC)| ≥2 and adjusted P values <0.01 were used in the next analysis stage (11)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "GSE53819 is a gene expression profile of HNSC and belongs to the Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version), which can be downloaded from the GEO database and executed on the GPL6480 platform (8).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35117201", "locator": "sections[3] \"Data source\" paragraph 2", "quote": "GSE53819 is a gene expression profile of HNSC and belongs to the Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version), which can be downloaded from the GEO database and executed on the GPL6480 platform (8)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Eleven module genes were prognostic in the HNSC TCGA/GTEx datasets.", "kind": "quantitative", "target": {"value": 2.0, "unit": "fold change", "tolerance": null, "source": "Using both |log2-fold change (FC)| ≥2 and adjusted P value <0.01 criteria, a total of 604 genes were identified from GSE53819, including 159 upregulated genes and 445 downregulated genes (Table 1)."}, "evidence": [{"asset": "source:pmid:35117201", "locator": "sections[15] \"Overall survival of hub genes\" paragraph 2", "quote": "We found that 11 module genes were prognostic in the HNSC datasets (built-in TGCA/GTEx), which is under GSE53819 HNSC samples (Figure 4)."}, {"asset": "source:pmid:35117201", "locator": "sections[12] \"Identification of DEGs\" paragraph 2", "quote": "Using both |log2-fold change (FC)| ≥2 and adjusted P value <0.01 criteria, a total of 604 genes were identified from GSE53819, including 159 upregulated genes and 445 downregulated genes (Table 1)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Eleven module genes were prognostic in the HNSC TCGA/GTEx datasets.", "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:35117201"], "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:GSE53819"], "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:GSE53819"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35117201", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tcr-20-805", "sha256": "sha256:615f75b158f09b06d1d3387e30954a8bd290af501fc922eb8d3aa31e70fa90b4", "bytes": 19916, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/tcr-20-805", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8798121", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"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": "GSE53819 is a gene expression profile of HNSC and belongs to the Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version), which can be downloaded from the GEO database and executed on the GPL6480 platform (8).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "GSE53819 is a gene expression profile of HNSC and belongs to the Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version), which can be downloaded from the GEO database and executed on the GPL6480 platform (8).", "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}}], "gaps": ["asset:data:geo:GSE53819 not downloaded", "asset:data:geo:GSE53819 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We used the Benjamini and Hochberg methods, genes with |log2-fold change (FC)| ≥2 and adjusted P values <0.01 were used in the next analysis stage (11)."}}, {"id": "method-2", "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": "Protein-protein interaction"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "build_graph", "expected_value": 2.0, "unit": "fold change", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. 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