Transcriptomic and functional network features of lung squamous cell carcinoma through integrative analysis of GEO and TCGA data.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30367091", "kind": "science-record", "revision": 8, "content_hash": "sha256:f59522879d5bba616419105284c8bc5383804827be2644acb893dcd2051faf78", "created_at": "2026-11-01T15:40:38Z", "updated_at": "2026-11-01T22:00:07Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptomic and functional network features of lung squamous cell carcinoma through integrative analysis of GEO and TCGA data.", "doi": "10.1038/s41598-018-34160-w", "pmid": "30367091", "authors": ["Yin Li", "Jie Gu", "Fengkai Xu", "Qiaoliang Zhu", "Di Ge", "Chunlai Lu"], "journal": "Scientific reports", "year": 2018, "abstract": "Lung squamous cell carcinoma (LUSC) is associated with poor clinical prognosis and lacks available targeted therapy. Novel molecules are urgently required for the diagnosis and prognosis of LUSC. Here, we conducted our data mining analysis for LUSC by integrating the differentially expressed genes acquired from Gene Expression Omnibus (GEO) database by comparing tumor tissues versus normal tissues (GSE8569, GSE21933, GSE33479, GSE33532, GSE40275, GSE62113, GSE74706) into The Cancer Genome Atlas (TCGA) database which includes 502 tumors and 49 adjacent non-tumor lung tissues. We identified intersections of 129 genes (91 up-regulated and 38 down-regulated) between GEO data and TCGA data. Based on these genes, we conducted our downstream analysis including functional enrichment analysis, protein-protein interaction, competing endogenous RNA (ceRNA) network and survival analysis. This study may provide more insight into the transcriptomic and functional features of LUSC through integrative analysis of GEO and TCGA data and suggests therapeutic targets and biomarkers for LUSC.", "claims": [{"id": "claim-method", "statement": "To see whether these 129 genes and DElncRNAs were related to prognostic significance, survival analysis was performed in the R environment using TCGAbiolinks11.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30367091", "locator": "sections[9] \"Survival analysis\" paragraph 2", "quote": "To see whether these 129 genes and DElncRNAs were related to prognostic significance, survival analysis was performed in the R environment using TCGAbiolinks11."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Here, we conducted our data mining analysis for LUSC by integrating the differentially expressed genes acquired from Gene Expression Omnibus (GEO) database by comparing tumor tissues versus normal tissues (GSE8569, GSE21933, GSE33479, GSE33532, GSE40275, GSE62113, GSE74706) into The Cancer Genome Atlas (TCGA) database which includes 502 tumors and 49 adjacent non-tumor lung tissues.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30367091", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here, we conducted our data mining analysis for LUSC by integrating the differentially expressed genes acquired from Gene Expression Omnibus (GEO) database by comparing tumor tissues versus normal tissues (GSE8569, GSE21933, GSE33479, GSE33532, GSE40275, GSE62113, GSE74706) into The Cancer Genome Atlas (TCGA) database which includes 502 tumors and 49 adjacent non-tumor lung tissues."}], "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:30367091"], "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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