Identification of hub genes and key modules in laryngeal squamous cell carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39145051", "kind": "science-record", "revision": 3, "content_hash": "sha256:0285054cdded96cfcd4b849517465e3dbc3d1264c013506affc1d888fb3d15cc", "created_at": "2026-11-01T20:29:15Z", "updated_at": "2026-11-01T22:12:29Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of hub genes and key modules in laryngeal squamous cell carcinoma.", "doi": "10.21037/tcr-24-104", "pmid": "39145051", "authors": ["Hongyue Li", "Shaojun Bo", "Yutian Guo", "Tiantian Wang", "Yangwang Pan"], "journal": "Translational cancer research", "year": 2024, "abstract": "Background: Laryngeal squamous cell carcinoma (LSCC) is the prominent cancer in head and neck, which greatly affects life quality of patients. The pathogenesis of LSCC is not clear. Presently, the LSCC treatments include chemotherapy, surgery and radiotherapy; however, these methods have poor efficacy in patients with recurrent and persistent cancer. Therefore, the study identified the hub genes accompanied with LSCC, which may be a potential therapeutic target in the future.\nMethods: We extracted whole transcriptome high-throughput sequencing (HTS) LSCC data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases and calculate differentially expressed genes (DEGs) between LSCC and normal samples using statistical software RStudio. Through weighted gene co-expression network analysis (WGCNA), enrichment examination of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and Gene Ontology (GO) functions, and examination of protein-protein interaction (PPI) network, we obtained network hub genes and validated the hub genes prognostic value and expression levels of protein.\nResults: Through analysis of differential gene expression, from the GEO and TCGA databases 2,139 and 2,774 DEGs were obtained, respectively, 13 and 15 modules were screened from TCGA-LSCC and GSE127165 datasets by WGCNA, respectively. The most significant positive and negative correlation modules in the WGCNA and DEG lists were overlapped, and overall 36 co-expressed overlapping genes were retrieved. Through enrichment analysis of GO and KEGG, it was found that the gene functions were highly concentrated in cell junction assembly, basement membrane, extracellular matrix (ECM) structural constituent etc., and the pathways were mainly concentrated in ECM receptor interaction, focal adhesion, small cell lung cancer, and toxoplasmosis. Through analysis of PPI network analysis, 10 network hub genes (SNAI2, ITGA6, LAMB3, LAMC2, CAV1, COL7A1, GJA1, EHF, OAT, and GPT) were obtained. Finally, survival analysis and protein expression validation of these genes confirmed that low OAT expression and high CAV1 expression remarkably influenced the survival of patient's prognosis with LSCC.\nConclusions: We recognized the hub genes and key modules nearly associated to LSCC and these genes were validated by survival analysis and the database of Human Protein Atlas (HPA), which is of high importance for unveiling the pathogenesis of LSCC and probing for new precise biological marker and potential therapeutic targets.", "claims": [{"id": "claim-method", "statement": "To validate the hub genes credibility, the interrelationship among overall survival (OS) and hub genes was tested by survival analysis of Kaplan-Meier. Using R package survival and survminer depending on TCGA database clinical data (32).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39145051", "locator": "sections[10] \"Hub genes prognostic value\" paragraph 2", "quote": "To validate the hub genes credibility, the interrelationship among overall survival (OS) and hub genes was tested by survival analysis of Kaplan-Meier. Using R package survival and survminer depending on TCGA database clinical data (32)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All expression matrices and correlated clinical data of LSCC were copied through the R package TCGAbioLinks (9) in TCGA database. Overall, 123 samples were collected, including 111 cases of LSCC and 12 cases of normal tissue (see Table 1).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39145051", "locator": "sections[4] \"Collation of data from TCGA and GEO database\" paragraph 2", "quote": "All expression matrices and correlated clinical data of LSCC were copied through the R package TCGAbioLinks (9) in TCGA database. Overall, 123 samples were collected, including 111 cases of LSCC and 12 cases of normal tissue (see Table 1)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Low OAT expression and high CAV1 expression were associated with survival prognosis in patients with LSCC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39145051", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Finally, survival analysis and protein expression validation of these genes confirmed that low OAT expression and high CAV1 expression remarkably influenced the survival of patient’s prognosis with LSCC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Low OAT expression and high CAV1 expression were associated with survival prognosis in patients with LSCC.", "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:39145051"], "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:GSE127165"], "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:GSE127165"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39145051", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tcr-24-104", "sha256": "sha256:b682acba7e2222e6ad470e444b04d9256c6daafcaa950bcafe318fc533d606eb", "bytes": 24464, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/tcr-24-104", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11319952", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE127165", "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=GSE127165", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE127165", "version": null, "note": "All expression matrices and correlated clinical data of LSCC were copied through the R package TCGAbioLinks (9) in TCGA database. Overall, 123 samples were collected, including 111 cases of LSCC and 12 cases of normal tissue (see Table 1).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All expression matrices and correlated clinical data of LSCC were copied through the R package TCGAbioLinks (9) in TCGA database. 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