Integrated bioinformatics analysis to identify key genes related to the prognosis of esophageal squamous cell carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35116493", "kind": "science-record", "revision": 5, "content_hash": "sha256:dce1ea230f0cf0da03fc02acd89a1706d6b57b078dee9fdc349f26cc91ce286a", "created_at": "2026-11-01T17:36:50Z", "updated_at": "2026-11-01T22:48:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated bioinformatics analysis to identify key genes related to the prognosis of esophageal squamous cell carcinoma.", "doi": "10.21037/tcr-20-3220", "pmid": "35116493", "authors": ["Ying Yang", "Zhiwei Sun", "Youwu Shi", "Jing Sun", "Xiaodong Zhang"], "journal": "Translational cancer research", "year": 2021, "abstract": "BACKGROUND: Esophageal squamous cell carcinoma (ESCC) is a serious threat to human health and life. The National Center for Biotechnology Information Gene Expression Omnibus (NCBI-GEO) database provides valuable information on genes related to the pathogenesis and prognosis of ESCC, which helps us to make in-depth understanding about the disease and improve its prognosis.\nMETHODS: Four microarray profiles [GSE77861 (African Americans), GSE26886 (Germans), GSE17351 (Americans), and GSE45670 (Chinese)] from the NCBI-GEO including 49 ESCC tissues and 41 corresponding normal tissues were collected. Integrated bioinformatics methods, including protein-protein interaction (PPI) network analysis, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, and Kaplan-Meier plotter were applied to determine the differentially expressed genes (DEGs) in ESCC together with their core functions and relationship with survival.\nRESULTS: A total of 220 upregulated and 112 downregulated genes were identified as DEGs in ESCC, of which, 40 upregulated genes were core function genes. The DEGs were mostly involved in DNA replication and cell cycle pathways. Survival analysis and Bonferroni adjustment showed kinesin family member 18A (KIF18A) and TTK protein kinase (TTK) to be related to prognosis in ESCC.\nCONCLUSIONS: The findings of the present study verified the previously proposed association between TTK and patient survival in ESCC, and identified KIF18A as ESCC prognosis-related gene markers for the first time. The underlying mechanism needs to be further investigated using larger sample size studies and biological experiments in future.", "claims": [{"id": "claim-method", "statement": "Associations between the identified hub genes and ESCC survival in public genome databases, including the European Genome-phenome Archive (EGA), The Cancer Genome Atlas (TCGA), and GEO (Affymetrix microarrays only), were evaluated using the online Kaplan-Meier plotter (17).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35116493", "locator": "sections[7] \"Survival analysis\" paragraph 2", "quote": "Associations between the identified hub genes and ESCC survival in public genome databases, including the European Genome-phenome Archive (EGA), The Cancer Genome Atlas (TCGA), and GEO (Affymetrix microarrays only), were evaluated using the online Kaplan-Meier plotter (17)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data used in our study are available in public databases, including the NCBI-GEO microarray database, EGA, and TCGA.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35116493", "locator": "sections[7] \"Survival analysis\" paragraph 3", "quote": "All data used in our study are available in public databases, including the NCBI-GEO microarray database, EGA, and TCGA."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Survival analysis and Bonferroni adjustment showed kinesin family member 18A (KIF18A) and TTK protein kinase (TTK) to be related to prognosis in ESCC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35116493", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Survival analysis and Bonferroni adjustment showed kinesin family member 18A (KIF18A) and TTK protein kinase (TTK) to be related to prognosis in ESCC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Survival analysis and Bonferroni adjustment showed kinesin family member 18A (KIF18A) and TTK protein kinase (TTK) to be related to prognosis in ESCC.", "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:35116493"], "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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