Identification of Key Modules and Hub Genes Involved in Esophageal Squamous Cell Carcinoma Tumorigenesis Using WCGNA.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33345608", "kind": "science-record", "revision": 5, "content_hash": "sha256:8b898068fb08424fccf82250916b4f7694ca4512ba2f4594078b28e6235a2ec5", "created_at": "2026-11-01T15:41:20Z", "updated_at": "2026-11-01T21:24:21Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Key Modules and Hub Genes Involved in Esophageal Squamous Cell Carcinoma Tumorigenesis Using WCGNA.", "doi": "10.1177/1073274820978817", "pmid": "33345608", "authors": ["Nanzheng Chen", "Guangjian Zhang", "Junke Fu", "Qifei Wu"], "journal": "Cancer control : journal of the Moffitt Cancer Center", "year": 2020, "abstract": "INTRODUCTION: The mechanistic basis for the development of esophageal squamous cell carcinoma (ESCC) remains poorly understood. The goal of the present study was thus to characterize mRNA and long noncoding RNA (lncRNA) expression profiles associated with ESCC in order to identify key hub genes associated with the pathogenesis of this cancer.\nMATERIALS AND METHODS: The GSE26866 and GSE45670 datasets from the Gene Expression Omnibus (GEO) database were used to conduct a weighted gene co-expression network analysis (WGCNA), after which Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted. Cytoscape was additionally used to construct lncRNA-mRNA networks, after which hub genes were identified and validated through the assessment of TCGA datasets and clinical samples.\nRESULTS: Two gene modules were found to be closely linked to ESCC tumorigenesis. These genes were enriched in cell cycle, MAPK signaling, JAK-STAT signaling, pyrimidine metabolism, arachidonic acid metabolism, and P53 signaling pathway activity, all of which are directly linked with the development of cancer. In total, we identified and validated 9 hub genes associated with ESCC (DDX18, DNMT1, NCAPG, WDHD1, PRR11, VOPP1, ZKSCAN5, LC35C2, and PHACTR2).\nCONCLUSION: In summary, we identified key gene modules and hub genes associated with ESCC development, and we constructed a lncRNA-mRNA network pertaining to this cancer type. These results provide a foundation for future research regarding the mechanistic basis of ESCC.", "claims": [{"id": "claim-method", "statement": "The GSE26866 and GSE45670 microarray datasets were downloaded from the NCBI Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/). Herein, we performed WGCNA by assessing co-expressed gene networks in the GSE26866 and GSE45670 datasets, leading to the identification of 7 gene co-expression modules.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33345608", "locator": "sections[3] \"Gene Expression Data and Preprocessing\" paragraph 2", "quote": "The GSE26866 and GSE45670 microarray datasets were downloaded from the NCBI Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/)."}, {"asset": "source:pmid:33345608", "locator": "sections[19] \"Discussion\" paragraph 4", "quote": "Herein, we performed WGCNA by assessing co-expressed gene networks in the GSE26866 and GSE45670 datasets, leading to the identification of 7 gene co-expression modules."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The GSE26866 and GSE45670 microarray datasets were downloaded from the NCBI Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/). The GSE26866 dataset included 9 ESSC and 19 normal samples, while the GSE45670 dataset contained 28 ESCC and 10 normal samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33345608", "locator": "sections[3] \"Gene Expression Data and Preprocessing\" paragraph 2", "quote": "The GSE26866 and GSE45670 microarray datasets were downloaded from the NCBI Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/). The GSE26866 dataset included 9 ESSC and 19 normal samples, while the GSE45670 dataset contained 28 ESCC and 10 normal samples."}], "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:33345608"], "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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