Molecular mechanism detection of stage I to stage II transition of esophageal squamous cell carcinoma: a system biology approach.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40406432", "kind": "science-record", "revision": 3, "content_hash": "sha256:299e67955f50a8fe1f3d614f655da46dcbd8ac9babb676f5d807a053cbda9a6a", "created_at": "2026-11-01T20:30:32Z", "updated_at": "2026-11-01T22:14:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Molecular mechanism detection of stage I to stage II transition of esophageal squamous cell carcinoma: a system biology approach.", "doi": "10.22037/ghfbb.v17i4.3013", "pmid": "40406432", "authors": ["Mitra Rezaei", "Fatemeh Bandarian", "Farideh Razi", "Zahra Razzaghi", "Ayad Bahadori Monfared", "Babak Arjmand", "Reza M Robati", "Alireza Ahmadzadeh"], "journal": "Gastroenterology and hepatology from bed to bench", "year": 2024, "abstract": "Aim: Molecular mechanism detection of stage I to stage II transition of esophageal squamous cell carcinoma via protein-protein interaction (PPI) network analysis is the main aim of this study.\nBackground: Esophageal cancer (EC) is recognized as cancer with a very poor prognosis and malignancy. It is characterized by a high prevalence rate within the world and a very low survival rate, even with treatment.\nMethods: To detect esophageal squamous cell carcinoma (ESCC) related genes, gene expression profiles (GEPs) of GSE161533 from the Gene Expression Omnibus (GEO) database were considered to be analyzed. Data was evaluated via the GEO2R program to explore the significant differential genes (DEGs) associated to stages I and II of esophageal squamous cell carcinoma. Each analysis's top 250 significant DEGs were evaluated, and the non-common genes were assessed via PPI network analysis. The hub-bottleneck DEGs were determined and enriched via gene ontology.\nResults: Results indicate 373 significant DEGs discriminate stage I from stage II. PPI network analysis associated with gene expression assessment showed that COL1A1, SERPINE1, PDGFRB, AURKA, TGFBI, LGALS3, BRCA1, and TFRC are the critical DEGs which are related to ESCC transition state from stage I to II of disease. A total of 13 biological processes and molecular functions were related to the crucial genes.\nConclusion: In conclusion, the Upregulation of COL1A1, SERPINE1, PDGFRB, AURKA, TGFB1, and LGALS3 and downregulation of BRCA1 and TFRC in stage II of ESCC relative to stage I were pointed out as the key events which are associated with promotion of stage I to stage II transition.", "claims": [{"id": "claim-method", "statement": "Padj < 0.05 was considered to explore the significant DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40406432", "locator": "sections[7] \"Statistical analysis\" paragraph 2", "quote": "Padj < 0.05 was considered to explore the significant DEGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "To detect esophageal squamous cell carcinoma related genes, gene expression profiles (GEPs) of GSE161533 from the GEO database (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse161533) were considered to be analyzed.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40406432", "locator": "sections[3] \"Data collection\" paragraph 2", "quote": "To detect esophageal squamous cell carcinoma related genes, gene expression profiles (GEPs) of GSE161533 from the GEO database (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse161533) were considered to be analyzed."}], "state": "complete"}, {"id": "claim-target-result", "statement": "373 significant DEGs discriminate stage I from stage II.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40406432", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Results indicate 373 significant DEGs discriminate stage I from stage II."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "373 significant DEGs discriminate stage I from stage II.", "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:40406432"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE161533"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE161533"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40406432", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.22037/ghfbb.v17i4.3013", "sha256": 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