Identification of four genes and biological characteristics of esophageal squamous cell carcinoma by integrated bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33602210", "kind": "science-record", "revision": 5, "content_hash": "sha256:5b9ce31dfdfad44ffcd6011448c452912a191af7aa221f2ccc91dfd8a320c7fc", "created_at": "2026-11-01T15:41:25Z", "updated_at": "2026-11-01T22:03:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of four genes and biological characteristics of esophageal squamous cell carcinoma by integrated bioinformatics analysis.", "doi": "10.1186/s12935-021-01814-1", "pmid": "33602210", "authors": ["Yexun Song", "Xianyao Wang", "Fengjun Wang", "Xiaowei Peng", "Peiyu Li", "Shaojun Liu", "Decai Zhang"], "journal": "Cancer cell international", "year": 2021, "abstract": "BACKGROUND: Esophageal squamous cell carcinoma (ESCC) has become one of the most serious diseases affecting populations worldwide and is the primary subtype of esophageal cancer (EC). However, the molecular mechanisms governing the development of ESCC have not been fully elucidated.\nMETHODS: The robust rank aggregation method was performed to identify the differentially expressed genes (DEGs) in six datasets (GSE17351, GSE20347, GSE23400, GSE26886, GSE38129 and GSE77861) from the Gene Expression Omnibus (GEO). The Search Tool for the Retrieval of Interacting Genes (STRING) database was utilized to extract four hub genes from the protein-protein interaction (PPI) network. Module analysis and disease free survival analysis of the four hub genes were performed by Cytoscape and GEPIA. The expression of hub genes was analyzed by GEPIA and the Oncomine database and verified by real-time quantitative PCR (qRT-PCR).\nRESULTS: In total, 720 DEGs were identified in the present study; these genes consisted of 302 upregulated genes and 418 downregulated genes that were significantly enriched in the cellular component of the extracellular matrix part followed by the biological process of the cell cycle phase and nuclear division. The primary enriched pathways were hsa04110:Cell cycle and hsa03030:DNA replication. Four hub genes were screened out, namely, SPP1, MMP12, COL10A1 and COL5A2. These hub genes all exhibited notably increased expression in ESCC samples compared with normal samples, and ESCC patients with upregulation of all four hub genes exhibited worse disease free survival.\nCONCLUSIONS: SPP1, MMP12, COL10A1 and COL5A2 may participate in the tumorigenesis of ESCC and demonstrate the potential to serve as molecular biomarkers in the early diagnosis of ESCC. This study may help to elucidate the molecular mechanisms governing ESCC and facilitate the selection of targets for early treatment and diagnosis.", "claims": [{"id": "claim-method", "statement": "Statistical significance between two groups was evaluated by Student’s t test between two groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33602210", "locator": "sections[9] \"Statistical analysis\" paragraph 2", "quote": "Statistical significance between two groups was evaluated by Student’s t test between two groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33602210", "locator": "sections[26] \"notes\" paragraph 1", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "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:33602210"], "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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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:33602210", "data:geo:GSE17351", "asset:table:pmid:33602210:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE17351"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:27:06Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 22518, "completion_tokens": 1989, "cached_tokens": 784}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:33602210", "type": "paper", "label": "pmid:33602210"}, {"id": "source:pmid:33602210", "type": "manuscript", "label": "PMID 33602210 full text"}, {"id": "data:geo:GSE17351", "type": "dataset", "label": "GEO GSE17351"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33602210", "type": "paper", "label": "pmid:33602210"}, {"id": "source:pmid:33602210", "type": "manuscript", "label": "PMID 33602210 full text"}, {"id": "data:geo:GSE17351", "type": "dataset", "label": "GEO GSE17351"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33602210", "type": "extraction", "used": ["source:pmid:33602210"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE17351", "type": "accession_resolution", "used": ["data:geo:GSE17351"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:33602210", "parent_hash": "sha256:7e46caf3b4ce398329cdcf4cdf7e2abdd5e30cc4ddd66ec295cd0a2ffebe19be", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE17351 licence not read", "asset:data:geo:GSE17351 not downloaded", "asset:data:geo:GSE20347 licence not read", "asset:data:geo:GSE20347 not downloaded", "asset:data:geo:GSE23400 licence not read", "asset:data:geo:GSE23400 not downloaded", "asset:data:geo:GSE26886 licence not read", "asset:data:geo:GSE26886 not downloaded", "asset:data:geo:GSE38129 licence not read", "asset:data:geo:GSE38129 not downloaded", "asset:data:geo:GSE77861 licence not read", "asset:data:geo:GSE77861 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["IA and the Oncomine database and verified by real-time quantitative PCR (qRT-PCR). RESULTS: In total, 720 DEGs were"], "order_basis": "paper_text_order:976", "id": "assay:1"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}