Identification of potential core genes in esophageal carcinoma using bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34232175", "kind": "science-record", "revision": 7, "content_hash": "sha256:55eca5f95d4cb8138c765a28c38721def490a61018160732e7a149756d84e198", "created_at": "2026-11-01T15:41:42Z", "updated_at": "2026-11-01T22:04:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of potential core genes in esophageal carcinoma using bioinformatics analysis.", "doi": "10.1097/MD.0000000000026428", "pmid": "34232175", "authors": ["Xiaojie Yang", "Mengyue Tian", "Weiguang Zhang", "Tianci Chai", "Zhimin Shen", "Mingqiang Kang", "Jiangbo Lin"], "journal": "Medicine", "year": 2021, "abstract": "BACKGROUND: Esophageal squamous cell carcinoma (ESCC) is a common human malignancy worldwide. The tumorigenesis mechanism in ESCC is unclear.\nMATERIALS AND METHODS: To explore potential therapeutic targets for ESCC, we analyzed 3 microarray datasets (GSE20347, GSE38129, and GSE67269) derived from the gene expression omnibus (GEO) database. Then, the GEO2R tool was used to screen out differently expressed genes (DEGs) between ESCC and normal tissue. Gene ontology function and kyoto encyclopedia of genes and genomes pathway enrichment analysis were performed using the database for annotation, visualization and integrated discovery to identify the pathways and functional annotation of DEGs. Protein-protein interaction of these DEGs was analyzed based on the search tool for the retrieval of interacting genes database and visualized by Cytoscape software. In addition, we used encyclopedia of RNA interactomes (ENCORI), gene expression profiling interactive analysis (GEPIA), and the human protein atlas to confirm the expression of hub genes in ESCC. Finally, GEPIA was used to evaluate the prognostic value of hub genes expression in ESCC patients and we estimated the associations between hub genes expression and immune cell populations (B Cell, CD8+ T Cell, CD4+ T Cell, Macrophage, Neutrophil, and Dendritic Cell) in esophageal carcinoma (ESCA) using tumor immune estimation resource (TIMER).\nRESULTS: In this study, 707 DEGs (including 385 upregulated genes and 322 downregulated genes) and 6 hub genes (cyclin B1 [CCNB1], cyclin dependent kinase 1 [CDK1], aurora kinase A [AURKA], ubiquitin conjugating enzyme E2C [UBE2C], cyclin A2 [CCNA2], and cell division cycle 20 [CDC20]) were identified. All of the 6 hub genes were highly expressed in ESCC tissues. Among of them, only CCNB1 and CDC20 were associated with stage of ESCC and all of them were not associated with survival time of patients.\nCONCLUSION: DEGs and hub genes were confirmed in our study, providing a thorough, scientific and comprehensive research goals for the pathogenesis of ESCC.", "claims": [{"id": "claim-data-access", "statement": "The datasets generated during and/or analyzed during the current study are publicly available.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34232175", "locator": "sections[18] \"fn-group\" paragraph 1", "quote": "The datasets generated during and/or analyzed during the current study are publicly available."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:34232175"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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"PMC8270608", "section_index": 10, "section_title": "Identification of differently expressed genes", "row_count": 4, "column_count": 4}, "table": {"label": "Table 1", "caption": "Statistics of tissues of 3 microarray database.", "rows": [["Dataset ID", "Tumor", "Normal", "Total number"], ["GSE20347", "17", "17", "34"], ["GSE38129", "30", "30", "60"], ["GSE67269", "73", "73", "146"]], "row_count": 4, "column_count": 4, "numeric_cells": 12, "header_rows": 1, "locator": "section[10]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:34232175:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:457bb0424ccba83ae61fe5ec7fb791626092667a90b8cda63cce69f82724bd06", "bytes": 350, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[2]#T2", "version": null, "note": "Statistics of DEGs of 3 microarray database.", "structure": {"pmcid": "PMC8270608", "section_index": 10, "section_title": "Identification of differently expressed genes", "row_count": 4, "column_count": 4}, "table": {"label": "Table 2", "caption": "Statistics of DEGs of 3 microarray database.", "rows": [["Dataset ID", "Upregulated genes", "downregulated genes", "DEGs"], ["GSE20347", "607", "716", "1323"], ["GSE38129", "500", "423", "923"], ["GSE67269", "495", "465", "960"]], "row_count": 4, "column_count": 4, "numeric_cells": 12, "header_rows": 1, "locator": "section[10]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:34232175:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f72658322afcd907f6f87dba84208a49ea7f10d219e6b9c0d553d6994dd264d5", "bytes": 1850, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#T3", "version": null, "note": "Significantly enriched GO terms and KEGG pathways of DEGs.", "structure": {"pmcid": "PMC8270608", "section_index": 11, "section_title": "Gene ontology and pathway functional enrichment analysis", "row_count": 26, "column_count": 5}, "table": {"label": "Table 3", "caption": "Significantly enriched GO terms and KEGG pathways of DEGs.", "rows": [["Category", "Term", "Description", "Count", "FDR"], ["BP term", "GO:0030198", "extracellular matrix organization", "37", "7.04E-12"], ["BP term", "GO:0051301", "cell division", "48", "5.19E-11"], ["BP term", "GO:0007067", "mitotic nuclear division", "36", "9.96E-09"], ["BP term", "GO:0042493", "response to drug", "32", "1.46E-04"], ["BP term", "GO:0007155", "cell adhesion", "39", "0.001202"], ["BP term", "GO:0008283", "cell proliferation", "30", "0.018629"], ["BP term", "GO:0008284", "positive regulation of cell proliferation", "35", "0.022819"], ["BP term", "GO:0055114", "oxidation-reduction process", "40", "0.049558"], ["CC term", "GO:0070062", "extracellular exosome", "182", "4.41E-13"], ["CC term", "GO:0005615", 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