Weighted Gene Correlation Network Analysis Identifies Specific Functional Modules and Genes in Esophageal Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34987580", "kind": "science-record", "revision": 4, "content_hash": "sha256:1522f6e0719ba88b2ee68b87ca12499b8d4708440ef65f30bf9b6ab4810bf498", "created_at": "2026-11-01T17:36:42Z", "updated_at": "2026-11-01T22:05:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Weighted Gene Correlation Network Analysis Identifies Specific Functional Modules and Genes in Esophageal Cancer.", "doi": "10.1155/2021/8223263", "pmid": "34987580", "authors": ["Wei Xu", "Jian Xu", "Zhiqiang Wang", "Yuequan Jiang"], "journal": "Journal of oncology", "year": 2021, "abstract": "OBJECTIVE: Esophageal cancer (ESCA) is one of the most aggressive malignancies globally with an undesirable five-year survival rate. Here, this study was conducted for determining specific functional genes linked with ESCA initiation and progression.\nMETHODS: Gene expression profiling of ESCA was curated from TCGA (containing 160 ESCA and 11 nontumor specimens) and GSE38129 (30 paired ESCA and nontumor tissues) datasets. Differential expression analysis was conducted between ESCA and nontumor tissues with adjusted p value <0.05 and |log2fold-change|>1. Weighted gene coexpression network analysis (WGCNA) was conducted for determining the ESCA-specific coexpression modules and genes. Thereafter, ESCA-specific differentially expressed genes (DEGs) were intersected. Functional enrichment analysis was then presented with clusterProfiler package. Protein-protein interaction was conducted, and hub genes were determined. Association of hub genes with pathological staging was evaluated, and survival analysis was presented among ESCA patients.\nRESULTS: This study determined 91 ESCA-specific DEGs following intersection of DEGs and ESCA-specific genes in TCGA and GSE38129 datasets. They were remarkably linked to cell cycle progression and carcinogenic pathways like the p53 signaling pathway, cellular senescence, and apoptosis. Ten ESCA-specific hub genes were determined, containing ASPM, BUB1B, CCNA2, CDC20, CDK1, DLGAP5, KIF11, KIF20 A, TOP2A, and TPX2. They were prominently associated with pathological staging. Among them, KIF11 upregulation was in relation to undesirable prognosis of ESCA patients.\nCONCLUSION: Collectively, we determined ESCA-specific coexpression modules and hub genes, which offered the foundation for future research concerning the mechanistic basis of ESCA.", "claims": [{"id": "claim-method", "statement": "Weighted gene coexpression network analysis (WGCNA) was conducted for determining the ESCA-specific coexpression modules and genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34987580", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Weighted gene coexpression network analysis (WGCNA) was conducted for determining the ESCA-specific coexpression modules and genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study are included within the supplementary information files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34987580", "locator": "sections[24] \"Data Availability\" paragraph 2", "quote": "The data used to support the findings of this study are included within the supplementary information files."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Ten ESCA-specific hub genes were determined, containing ASPM, BUB1B, CCNA2, CDC20, CDK1, DLGAP5, KIF11, KIF20 A, TOP2A, and TPX2.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34987580", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Ten ESCA-specific hub genes were determined, containing ASPM, BUB1B, CCNA2, CDC20, CDK1, DLGAP5, KIF11, KIF20 A, TOP2A, and TPX2."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Ten ESCA-specific hub genes were determined, containing ASPM, BUB1B, CCNA2, CDC20, CDK1, DLGAP5, KIF11, KIF20 A, TOP2A, and TPX2.", "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:34987580"], "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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