Identification of key genes for esophageal squamous cell carcinoma via integrated bioinformatics analysis and experimental confirmation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32642240", "kind": "science-record", "revision": 8, "content_hash": "sha256:978d7645aaa14e688cd692df185617e1b7bf6621ad01e50650c951d3f2a86037", "created_at": "2026-11-01T15:41:05Z", "updated_at": "2026-11-01T22:01:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of key genes for esophageal squamous cell carcinoma via integrated bioinformatics analysis and experimental confirmation.", "doi": "10.21037/jtd.2020.01.33", "pmid": "32642240", "authors": ["Jia Hu", "Rongzhen Li", "Huikai Miao", "Zhesheng Wen"], "journal": "Journal of thoracic disease", "year": 2020, "abstract": "BACKGROUND: Esophageal squamous cell carcinoma (ESCC) as the main subtype of esophageal cancer (EC) is a leading cause of cancer-related death worldwide. Despite advances in early diagnosis and clinical management, the long-term survival of ESCC patients remains disappointing, due to a lack of full understanding of the molecular mechanisms.\nMETHODS: In order to identify the differentially expressed genes (DEGs) in ESCC, the microarray datasets GSE20347 and GSE26886 from Gene Expression Omnibus (GEO) database were analyzed. The enrichment analyses of gene ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Set Enrichment Analysis (GSEA) were performed for the DEGs. The protein-protein interaction (PPI) network of these DEGs was constructed using the Cytoscape software based on the STRING database to select as hub genes for weighted co-expression network analysis (WGCNA) with ESCC samples from TCGA database.\nRESULTS: A total of 746 DEGs were commonly shared in the two datasets including 286 upregulated genes and 460 downregulated genes in ESCC. The DEGs were enriched in biological processes such as extracellular matrix organization, proliferation and keratinocyte differentiation, and were enriched in biological pathways such as ECM-receptor interaction and cell cycle. GSEA analysis also indicated the enrichment of upregulated DEGs in cell cycle. The 40 DEGs were selected as hub genes. The MEblack module was found to be enriched in the cell cycle, Spliceosome, DNA replication and Oocyte meiosis. Among the hub genes correlated with MEblack module, GSEA analysis indicated that DEGs of TCGA samples with DLGAP5 upregulation was enriched in cell cycle. Moreover, the highly endogenous expression of DLGAP5 was confirmed in ESCC cells. DLGAP5 knockdown significantly inhibited the proliferation of ESCC cells.\nCONCLUSIONS: DEGs and hub genes such as DLGAP5 from independent datasets in the current study will provide clues to elucidate the molecular mechanisms involved in development and progression of ESCC.", "claims": [{"id": "claim-method", "statement": "The student’s t test was used to compare the differences among different groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32642240", "locator": "sections[10] \"Statistical analysis\" paragraph 2", "quote": "The student’s t test was used to compare the differences among different groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original microarray data were downloaded from the GEO database (12). The GSE20347 based on GPL571 platform (Affymetrix Human Genome U133A 2.0 Array) contains 17 paired ESCC samples and normal adjacent esophageal tissues.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32642240", "locator": "sections[3] \"Microarray data collection\" paragraph 2", "quote": "The original microarray data were downloaded from the GEO database (12). The GSE20347 based on GPL571 platform (Affymetrix Human Genome U133A 2.0 Array) contains 17 paired ESCC samples and normal adjacent esophageal 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:32642240"], "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:GSE20347"], "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:GSE20347"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32642240", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/jtd.2020.01.33", "sha256": "sha256:f65f0c96e12e00b20705adf9c6a5d76058c9f3dac19a6cb3e9fa8dbb0434a132", "bytes": 25202, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/jtd.2020.01.33", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7330802", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE20347", "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=GSE20347", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE20347", "version": null, "note": "The original microarray data were downloaded from the GEO database (12). 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DLGAP5 knockdown significantly inhibited the proliferation of", "e.org/gsea/index.jsp) (17). Cell culture and transfection ESCC cell lines including TE-1, KYSE30 and K", "with DLGAP5 knockdown, TE-1 and KYSE410 were transfected with psi-LVRU6GP vectors with DLGAP5 shRNAs", "', sh-3#: 5'- CCATATTTCAGAAATATCCTC-3'). 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